Abstract
Main conclusion
Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet.
Abstract
Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
No datasets were generated or analysed during the current study.
References
Abbai R, Singh VK, Nachimuthu VV, Sinha P, Selvaraj R, Vipparla AK, Singh AK, Singh UM, Varshney RK, Kumar A (2019) Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic grains. Plant Biotechnol J 17:1612–1622. https://doi.org/10.1111/pbi.13087
Abrouk M, Ahmed HI, Cubry P et al (2020) Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 11:4488. https://doi.org/10.1038/s41467-020-18329-4
Aher RR, Reddy PS, Bhunia RK, Flyckt KS, Shankapal AR, Ojha R, Everard JD, Wayne LL, Ruddy BM, Deonovic B, Gupta SK, Sharma KK, Bhatnagar-Mathur P (2022) Loss-of-function of triacylgyycerol lipases are associated with low flour rancidity in pearl millet [Pennisetum glaucum (L.) R. Br.]. Front Plant Sci 13:962667. https://doi.org/10.3389/fpls.2022.962667
Almutairi (2022) Characterization and expression analysis of B12D-Like gene from pearl millet. Evol Bioinform 18:11769343221142284. https://doi.org/10.1177/11769343221142285
Amin N, Ahmad N, Wu N, Pu X, Ma T, Du Y, Bo X, Wang N, Sharif R, Wang P (2019) CRISPR-Cas9 mediated targeted disruption of FAD2-2 microsomal omega-6 desaturase in soybean (Glycine max L.). BMC Biotechol 19:9. https://doi.org/10.1186/s12896-019-0501-2
Anuradha N, Satyavathi CT, Meena MC, Sankar SM, Bharadwaj C, Bhat J et al (2017) Evaluation of pearl millet [Pennisetum glaucum (L.) R. Br.] for grain iron and zinc content in different agro climatic zones of India. Indian J Genet Plant Breed 77:65–73. https://doi.org/10.5958/0975-6906.2017.00009.8
Arrones A, Vilanova S, Plazas M, Mangino G, Pascual L, Díez MJ, Prohens J, Gramazio P (2020) The dawn of the age of multi-parent MAGIC populations in plant breeding: novel powerful next-generation resources for genetic analysis and selection of recombinant elite material. Biology 9:229. https://doi.org/10.3390/biology9080229
Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S (2019) Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor Appl Genet 132:1–25
Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S (2020) Detecting CSSLs and yield QTLs with additive, epistatic and QTL × environment interactions effects from Oryza sativa × Oryza nivara IRGC81832 cross. Sci Rep 10:7766. https://doi.org/10.1038/s41598-020-64300-0
Bandillo N, Raghavan C, Muyco PA, Sevilla MA et al (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice (n y) 6:11. https://doi.org/10.1186/1939-8433-6-11
Basava RK, Hash CT, Mahendrakar MD, Kishor PBK, Satyavathi CT, Kumar S et al (2019) Discerning combining ability loci for divergent environments using chromosome segment substitution lines (CSSLs) in pearl millet. PLoS ONE 14:e0218916. https://doi.org/10.1371/journal.pone.0218916
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30:555–561. https://doi.org/10.1038/nbt.2196
Berthouly-Salazar C, Thuillet AC, Rhoné B, Mariac C, Ousseini IS, Couderc M, Tenaillon MI, Vigouroux Y (2016) Genome scan reveals selection acting on genes linked to stress response in wild pearl millet. Mol Ecol 25:5500–5512. https://doi.org/10.1111/mec.13859
Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 15:346–354. https://doi.org/10.1038/nature22011
Bhargavi HA, Singh SP, Goswami S, Yadav S, Aavula N, Shashikumara P, Singhl T, Sankar SM, Danakumara T, Hemanth S, Kapoor C, Singh N (2024) Deciphering the genetic variability for biochemical parameters influencing rancidity of pearl millet (Pennisetum glaucum L. R. Br.) flour in a set of highly diverse lines and their categorization using ramcidity matrix. J Food Compos Anal 128:106035. https://doi.org/10.1016/j.jfca.2024.106035
Bhat JA, Karikari B, Adeboye KA et al (2022) Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. Theor Appl Genet 135:2407–2422. https://doi.org/10.1007/s00122-022-04120-0
Bidinger FR, Mahalakshmi V, Rao GDP (1987) Assessment of drought resistance in pearl millet [Pennisetum americanum (L.) Leeke]. I. Factors affecting yield under stress. Aust Agric Res 38:37–48. https://doi.org/10.1071/AR9870037
Boatwright JL, Brenton ZW, Boyles RE, Sapkota S, Myers MT, Jordan KE, Dale SM, Shakoor N, Cooper EA, Morris GP, Kresovich S (2021) Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics. G3 Genes Genomes Genet 11:4. https://doi.org/10.1093/g3journal/jkab060
Bohra A, Kilian B, Sivasankar S, Caccamo M, Mba C, Mccouch SR, Varshney RK (2021) Reap the crop wild relatives for breeding future crops. Trends Biotech 40:412–431. https://doi.org/10.1016/j.tibtech.2021.08.009
Brant EJ, Baloglu MC, Parikh A, Altpeter F (2021) CRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angle. Biotechnol J 16:e2100237. https://doi.org/10.1002/biot.202100237
Brinton J, Ramirez-Gonzalez RH, Simmonds J et al (2020) A haplotype-led approach to increase the precision of wheat breeding. Commun Biol 3:712. https://doi.org/10.1038/s42003-020-01413-2
Brunken JN (1977) A systematic study of Pennisetum sect. Pennisetum (Gramineae). Am J Bot 64:161–176. https://doi.org/10.2307/2442104
Brunken B, Jere N, de Wet JMJ, Harlan JR (1977) The morphology and domestication of pearl millet. Econ Bot 31:163–174. https://doi.org/10.1007/BF02866587
Burgarella C, Curby P, Kane NA, Varshney RK, Mariac C, Liu X, Shi C, Thudi M, Couderc M, Xu X, Chitikineni A, Scarcelli N, Barnaud A, Rhone B, Dupuy C, Francois O, Salazar CB, Vigouroux Y (2018) A western Sahara centre of domestication inferred from pearl millet genomes. Nat Ecol Evol 2:1377–1380
Cai Z, Liu H, He Q, Pu M, Chen J, Lai J, Li X, Jin W (2014) Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatic Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping. BMC Genomics 15:1025
Cardi T, Murovec J, Bakhsh A, Boniecka J et al (2023) CRISPR/Cas-mediated plant genome-editing: outstanding challenges a decade after implementation. Trends Plant Sci 28:1144–1165. https://doi.org/10.1016/j.tplants.2023.05.012
Ceasar A (2022) Genome-editing in millets: current knowledge and future perspectives. Mol Biol Rep 49:773–781. https://doi.org/10.1007/s11033-021-06975-w
Chakraborty A, Viswanath A, Malipatil R, Semalaiyappan J, Shah P, Ronanki S, Rathore A, Singh SP, Govidaraj M, Tonapi VA, Nepolean T (2022) Identification of candidate genes regulating drought tolerance in pearl millet. Int J Mol Sci 23:6907. https://doi.org/10.3390/ijms23136907
Champion L, Hohn A, Neumann K, Franke G, Breunig P (2023) A question of rite-pearl millet consumption at Nok culture sites, Nigeria (second/first millennium BC). Veg Hist Archaeobot 32:263–283
Chen K, Wang Y, Zhang R, Zhang H, Gao C (2019) CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual Rev Plant Biol 70:667–697. https://doi.org/10.1146/annurev-arplant-050718-100049
Cheng Z, Sun Y, Yang S, Zhi H, Yin T, Ma X, Zhang H, Diao X, Guo Y, Li X, Wu C, Sui Y (2021) Establishing in planta haploid inducer line by edited SiMTL in foxtail millet (Setaria italica). Plant Biotechnol J 19:1089–1109. https://doi.org/10.1111/pbi.13584
Choudhary M, Jayanand, Padaria JC (2015) Transcriptional profiling of pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially drought responsive genes. Physiol Mol Biol Plants 21:187–196. https://doi.org/10.1007/s12298-015-0287-1
Crossa J, Jarquin D, Franco J et al (2016) Genomic prediction of gene bank wheat landraces. G3 (bethesda) 6:1819–1834. https://doi.org/10.1534/g3.116.029637
Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de Los CG, Burgueño J, González-Camacho JM, Pérez-Elizalde S, Beyene Y, Dreisigacker S, Singh R, Zhang X, Gowda M, Roorkiwal M, Rutkoski J, Varshney RK (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975. https://doi.org/10.1016/j.tplants.2017.08.011
D’Andrea AC, Casey J (2002) Pearl millet and Kintampo subsistence. African Archae Rev 19:147–173. https://doi.org/10.1023/A:1016518919072
Dafaallah AB (2019) Biology and physiology of witchweed (Striga spp.): a review. Int J Acad Multidiscip Res 3:42–51
de Azevedo Peixoto L, Moellers TC, Zhang J, Lorenz AJ, Bhering LL, Beavis WD, Singh AK (2017) Leveraging genomic prediction to scan germplasm collection for crop improvement. PLoS ONE 12:e0179191. https://doi.org/10.1371/journal.pone.0179191
de Carvalho Ade O, Soares DJ, do Carmo MG, da Costa AC, Pimentel C (2006) Description of the life-cycle of the pearl millet rust fungus-Puccinia substriata var. penicillariae with a proposal of reducing var. indica to a synonym. Mycopathologia 161:331–336. https://doi.org/10.1007/s11046-006-0022-0. (PMID: 16649083)
Dempewolf H, Baute G, Anderson J, Kilian B, Smith C, Guarino L (2017) Past and future use of wild relatives in crop breeding. Crop Sci 57:1070–1082. https://doi.org/10.2135/cropsci2016.10.0885
Dhugga KS (2022) Gene editing to accelerate crop breeding. Front Plant Sci 13:889995. https://doi.org/10.3389/fpls.2022.889995
Djanaguiraman M, Perumal R, Ciampitti IA, Gupta SK, Prasad PVV (2017) Quantifying pearl millet response to high temperature stress: thresholds, sensitive stages, genetic variability and relative sensitivity of pollen and pistil. Plant Cell Environ 41:993–1007. https://doi.org/10.1111/pce.12931
Dudhate A, Shinde H, Tsugama D, Liu S, Takano T (2018) Transcriptomic analysis reveal the differentially expressed genes and pathways involved in drought tolerance in pearl millet [Pennisetum glaucum (L.) R. Br.]. 13:e0195908. https://doi.org/10.1371/journal.pone.0195908
Dujardin M, Hanna WW (1983) Apomictic and sexual pearl millet × Pennisetum squamulatum hybrids. J Hered 74:277–279. https://doi.org/10.1093/oxfordjournals.jhered.a109783
Dujardin M, Hanna W (1984) Microsporogenesis, reproductive behaviour and fertility in five Pennisetum species. Theor App Genet 67:197–201
Dujardin M, Hanna WW (1987) Inducing male fertility in crosses between pearl millet and Pennisetum orientale Rich. Crop Sci 27:65–68. https://doi.org/10.2135/cropsci1987
Dujardin M, Hanna WW (1989) Crossability of pearl millet with wild Pennisetum species. Crop Science 29:
Duke JA (1983) Cenchrus ciliaris L. Handbook of Energy Crops [Unpublished]. Purdue University, Center for New Crops & Plants Products. http://www.hort.purdue.edu/newcrop/duke_energy/Cenchrus_ciliaris.html
Dzievit MJ, Guo T, Xi X, Yu J (2021) Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize. Plant Genome 14:c20160. https://doi.org/10.1002/tpg2.20160
Elkonin LA, Gerashchenkov GA, Borisenko NV, Kenzhegulov OA, Kh SS, Rozhnova NA, Panin VM (2023) Development of sorghum mutants with improved in vitro protein digestibility by CRISPR/Cas9 editing of kafirin genes. Crop J 11:1411–1418. https://doi.org/10.1016/j.cj.2023.02.005
Eyland D, Luchaire N, Cabrera-Bosquet L, Parent B, Janssens SB, Swennen R, Welcker C, Tardieu F, Carpentier SC (2022) High-throughput phenotyping reveals differential transpiration behaviour within the banana wild relatives highlighting diversity in drought tolerance. Plant Cell Environ 45:1647–1663. https://doi.org/10.1111/pce.14310
FAO (2020) http://www.fao.org/faostat/en/#data/QC
Farrell HL, Funk J, Law D, Gornish ES (2020) Impact of drought and native grass competition on bufflegrass (Pennisetum ciliare). Biol Invasions 24:1–12. https://doi.org/10.1007/s10530-021-02671-9
Fernandez CGT, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D (2022) Pangenomes as a resource to accelerate breeding of under-utilized crop species. Int J Mol Sci 23:2671. https://doi.org/10.3390/ijms23052671
Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage-disequilibrium in plants. Annu Rev Plant Biol 54:357–374. https://doi.org/10.1146/annurev.arplant.54.031902.134907
Gobena D, Shimels M, Rich PJ, Spira CR, Bouwmeester H, Kanuganti S, Mengiste T, Ejeta S (2017) Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance. Proc Natl Acad Sci USA 114:4471–4476. https://doi.org/10.1073/pnas.1618965114
Goel S, Chen Z, Akiyama Y, Conner JA, Basu M (2006) Comparative physical mapping of the apospory-specific genomic region in two apomictic grasses Pennisetum squamulatum and Cenchrus ciliaris. Genetics 173:389–400
Golicz A, Bayer P, Barker G et al (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390. https://doi.org/10.1038/ncomms13390
Gorjanc G, Jenko J, Hearne SJ et al (2016) Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations. BMC Genomics 17:30. https://doi.org/10.1186/s12864-015-2345-z
Goud CA, Satturu V, Malipatil R, Viswanath A, Semalaiyappan J, Kudapa H, Rathod S, Rahtore A, Govindaraj M, Nepolean T (2022) Identification of iron and zinc responsive genes in pearl millet using genome-wide RNA-sequencing approach. Front Nutr 9:884381. https://doi.org/10.3389/fnut.2022.884381
Goyal P, Chugh LK (2017) Shelf life determinants and enzyme activities of pearl millet: a comparison of changes in stored flour of hybrids, CMS lines, inbreds and composites. J Food Sci Technol 54:3161–3169. https://doi.org/10.1007/s13197-017-2752-z
Guo L, Qiu J, Ye C et al (2017) Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat Commun 8:1031. https://doi.org/10.1038/s41467-017-01067-5
Guo Y, Liu L, Yue Y, Fan X, Teng W, Zhang H, Gao K, Guan J, Chang Z, Teng K (2022) Development of SSR markers based on transcriptome sequencing and verification of their conservation across species of ornamental Pennisetum Rich. (Poaceae). Agronomy 12:1683. https://doi.org/10.3390/agronomy12071683
Gupta SK, Rai KN, Singh P, Ameta VL, Gupta SK, Jayalekha AK, Mahala RS, Pareek S, Swami ML, Verma YS (2015) Seed set variability under high temperatures during flowering period in pearl millet (Pennisetum glaucum L. (R.) Br.). Field Crop Res 171:41–53. https://doi.org/10.1016/j.fcr.2014.11.005
Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1–13. https://doi.org/10.1007/s10681-007-9363-0
Halilou O, Assefa Y, Falalou H, Abdou H, Achirou BF, Karami SMA, Jagadish SVK (2020) Agronomic performance of pearl millet genotypes under variable phosphorus, water and environmental regimes. Agrosyst Geosci Environ 3:e20131. https://doi.org/10.1002/agg2.20131
Hammons RO (1970) Registration of Spancross peanuts (Reg. no.3). Crop Sci 10:459–460. https://doi.org/10.2135/cropsci1970.0011183X001000040056x
Hanna WW (1979) Interspecific hybrids between pearl millet and fountain grass. J Hered 70:425-427
Hanna WW (1989) Characteristics and stability of a new cytoplasmic-nuclear male sterile source in pearl millet. Crop Sci 29:1457–1459. https://doi.org/10.2135/cropsci1989
Hanna WW (1990) Transfer of germplasm from the secondary to the primary gene pool in pennistum. Theor Appl Genet 80:200–204. https://doi.org/10.1007/BF00224387
Hanna WW, Dujardin M (1982) Apomictic interspecific hybrids between pearl millet and Pennsietum orientale L.C. Rich. Crop Sci 22:857–859. https://doi.org/10.2135/cropsci1982.0011183X002200040038x
Hanna WW, Dujardin M (1986) Cytogenetics of Pennisetum schweinfurthii Pilger and its hybrids with pearl millet. Crop Sci 26:449–453. https://doi.org/10.2135/cropsci1986
Hanna WW, Wells HD, Burton GW (1987) Registration of pearl millet inbred parental lines Tift 85D2A1 and Tift 85D2B1. Crop Sci 27:1324–1325
Hao J, Yang Y, Futrell S, Kelly EA, Lorts CM, Nebie B, Runo S, Yang J, Alvarez S, Lasky JR, Schachtman DP (2023) CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage diooxygenese (CCD) genes in sorghum alters strigolactone biosynthesis and plant biotic interactions. Phytobiomes J 7:2471–2906. https://doi.org/10.1094/PBIOMES-08-22-0053-R
Harlan JR (1975) Crops and Man. American Society of Agronomy, Crop Science Society of America, Madison
Harlan JR (1992) Indigenous African agriculture. In: Cowan CW, Watson PJ (eds) The origins of agriculture. Smithsonian Institution, Washington, pp 59–70
Harlan JR, de Wet JMJ (1971) Toward a rational classification of cultivated plants. Taxonomy 20:509–517. https://doi.org/10.2307/1218252
Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Gruter S et al (2018) Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res 25:39–47. https://doi.org/10.1093/dnares/dsx036
Haussmann BIG, Parzies HK, Presterl T, Susjic Z, Miedaner T (2004) Plant genetic resources in crop improvement. Plant Genet Resour 2:3–21
He S, Liu H, Zhan J, Meng Y, Wang Y, Wang F, Ye G (2022) Genomic prediction using composite training sets is an effective method for exploiting germplasm conserved in rice gene banks. Crop J 10:1073–1082. https://doi.org/10.1016/j.cj.2021.11.011
Hittalmani S, Mahesh HB, Shirke MD et al (2017) Genome and transcriptome sequence of finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties. BMC Genomics 18:465. https://doi.org/10.1186/s12864-017-3850-z
Holker AC, Mayer M, Presterl T, Bauer E, Ouzunova M, Melchinger AE, Schon CC (2022) Theoretical and experimental assessment of genome-based prediction in landraces of allogamous crops. Proc Natl Acad Sci USA 3:e2121797119. https://doi.org/10.1073/pnas.2121797119
Horsnell R, Leigh FJ, Wright Tally IC, Burridge AJ, Ligeza A, Przewieslik-Allen AM, Howell P, Uauy C, Edwards KJ, Bentley AR (2023) A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation. Plant Genome. https://doi.org/10.1002/tpg2.20288
Hu Z, Mbacke B, Perumal R, Gueye MC, Sy O, Bouchet S, Prasad PVV, Morris GP (2015) Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): comparative analysis of global accessions and Senegalese landraces. BMC Genomics 16:1048. https://doi.org/10.1186/s12864-015-2255-0
Hu H, Yuan Y, Bayer PE, Fernandez CT, Scheben A, Golicz AA, Legume ED (2020) Pangenome construction using an iterative mapping and assembly approach. Methods Mol Biol 2107:35–47. https://doi.org/10.1007/978-1-0716-0235-5_3
Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotech J 10:826–839. https://doi.org/10.1111/j.1467-7652.2012.00702.x
Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM et al (2021) De novo assembly, annotation and comparative analysis of 26 diverse maize genomes. Science 373: 655-662. https://doi.org/10.1126/science.abg5289
Hurgobin B, Golicz AA, Bayer PE, Chan Chon-Kit K, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin Isobel AP, Pires Chris J, Chalhoub B, King GJ, Snowdon R, Batley J, Edward D (2018) Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnol J. https://doi.org/10.1111/pbi.12867
Jade SS, Takawale PS, Bahulikar RA (2021) The utility of ISSRs for the identification of interspecific hybrids between pearl millet (Pennisetum glaucum L. R. Br.) x napier grass (Pennisetum purpureum Schumach) plant genetic resources: characterization and utilization. Plant Genet 19:104–111. https://doi.org/10.1017/S1479262121000149
Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, Kheni J, Angadi UB, Iquebal MA, Golakia BA, Rai A, Kumar D (2018) Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources. Sci Rep 8:3382. https://doi.org/10.1038/s41598-018-21560-1
Jarquin D, Howard R, Liang Z, Gupta SK, Schanble JC, Crossa J (2020) Enhancing hybrid prediction in pearl millet with geomic and or multi-environment phenotpyping information on inbreds. Front Genet 10:1294. https://doi.org/10.3389/fgene.2019.01294
Jauhar PP (1973) Inter and intragenomal chromosome relationships in Pennisetum hybrid. In: 13th International Genet Congr Genetics 74:S126
Jauhar PP (1968) Inter and intragenomal chromosomal pairing in an interspecific hybrid and its bearing on the basic chromosome number in Pennisetum. Genetica 39:360–370
Jauhar PP (1981a) Cytogenetics and breeding of pearl millet and related species. Alan R. Liss, New York, p 91
Jauhar PP (1981b) Cytogenetics of pearl millet. Adv Agron 34:407–470
Jauhar PP, Hanna WW (1998) Cytogenetics and genetics of pearl millet. Adv Agron 64:1–26
Jauhar PP, Joppa LR (1996) Chromosome pairing as a tool in genome analysis: merits and limitations In: Jauhar PP (ed) Methods of genome analysis in plants. CRC Press, Inc, New York, pp 9-39
Jensen SE, Charles JR, Muleta K, Bradbury PJ, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney RK, Morris GP, Pressoir G, Buckler ES, Ramstein GP (2020) A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. Plant Genome 13:e20009. https://doi.org/10.1002/tpg2.20009
Jia G, Huang X, Zhi H et al (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961. https://doi.org/10.1038/ng.2673
Jordan KW, Bradbury Peter J, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E et al (2022) Development of the wheat practical haplotype graph database as a resource for genotyping data storage and genotype imputation. G3 Genes Genomes Genet 12:jkab390. https://doi.org/10.1093/g3journal/jkab390
Kanfany G, Serba DD, Rhodes D, St AP, Bernardo A, Gangashetty PI, Kane NA, Bai G (2020) Genomic diversity in pearl millet inbred lines derived from landraces and imnproved varieties. BMC Genomics 21:469. https://doi.org/10.1186/s12864-020-06796-4
Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT et al (2008) Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breed 127:33–37
Kapoor C, Singh SP, Sankar MS, Singh N (2022) Enhancing drought tolerance in pearl millet: integrating traditional and omics approaches. Euphytica 218:104. https://doi.org/10.1007/s10681-022-03045-5
Kaushal P, Roy AK, Khare A, Malaviya DR, Zadoo SN, Choubey RN (2007) Crossability and characterization of interspecific hybrids between sexual Pennisetum glaucum (Pearl millet) and a new cytotype (2n=56) of apomictic P. squamulatum. Cytologia 72:111–118
Kaushal P, Khare A, Zadoo SN, Roy AK, Malaviya DR, Agrawal A et al (2008) Sequential reduction of Pennisetum squamulatum genome complement in P. glaucum (2n = 28) × P. squamulatum (2n = 56) hybrids and their progenies revealed its octoploid status. Cytologia 73:151–158
Kaushal P, Dwivedi KK, Radhakrishna A, Srivastava MK, Malaviya DR, Roy AK, Saxena S, Paul S (2014) Development and characterization of a hexaploid Pennisetum orientale (2n=6x=54) cytotype recovered through BIII hybridization. Cytologia 80:37–43
Kaushik P, Prohens J, Vilanova S, Gramazio P, Plazas M (2016) Phenotyping of eggplant wild relatives and interspecific hybrids with conventional and phenomics descriptors provides insight for their potential utilization in breeding. Front Plant Sci 7:677. https://doi.org/10.3389/fpls.2016.00677
Kharrat-Souissi A, Baumel A, Torre F, Juin M, Siljak-Yakovlev S, Roig A, Chaieb M (2011) New insights in to the polyploid complex Cenchrus ciliaris L. (Poaceae) show its capacity for gene flow and recombination processes despite its apomictic nature. Aust J Bot 59:543–553
Knox JW, Hess TM, Daccache A, Perez OM (2011) What are the projected impacts of climate change on food crop productivity in Africa and South Asia? DFID systematic review final report. Cranfield University, Cranfield, Bedfordshire, UK, p 77
Kountche BA, Hash CT, Dodo H, Laoualy O, Sanogo MD, Timbeli A, Vigouroux Y, This D, Nijkamp R, Haussmann BIG (2013) Development of a pearl millet Striga-resistant genepool: Response to five cycles of recurrent selection under Striga-infested field conditions in West Africa. Field Crops Res 154:82–90. https://doi.org/10.1016/j.fcr.2013.07.008
Kumar N, Boatwright JL, Brenton ZW, Sapkota S, Ballen-Taborda C, Myers MT, Cox WA, Jordan KE, Kresovich S, Boyles RE (2023) Development and characterization of a sorghum mulit-parent advanced generation intercross (MAGIC) population for capturing diversity among seed parent gene pool. G3 Genes Genomes Genet 13:4. https://doi.org/10.1093/g3journal/jkad037
Kumari BR, Kolesnikova-Allen MA, Hash CT, Senthilvel S, Nepolean T, Kishor Kavi PB, Riera-Lizarazu O, Witcombe JR, Srivastava RK (2014) Development of a set of chromosome segment substitution lines in pearl millet [Pennisetum glaucum (L.) R. Br.]. Crop Sci 54:2175–2182
Lakis G, Navascues M, Rekima S, Simon M, Remigereau MS, Leveugle M, Takvorian N, Lamy F, Depaulis F, Robert T (2012) Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication. PLoS ONE 7:e36642. https://doi.org/10.1371/journal.pone.0036642
Lehermeier C, Kramer N, Bauer E, Bauland C, Camisan C, Campo L, Flament P, Melchinger AE, Menz M, Meyer N, Moreau L, Moreno-González J, Ouzunova M, Pausch H, Ranc N, Schipprack W, Schonleben M, Walter H, Charcosset A, Schon CC (2014) Usefulness of multiparental populations of maize (Zea mays L.) for genome-based prediction. Genetics 198:3–16. https://doi.org/10.1534/genetics.114.161943
Li Y-H, Zhou G, Ma J, Jiang W, Jin L-G, Zhang Z, Guo Y et al (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1052. https://doi.org/10.1038/nbt.2979
Li X, Wang W, Wang Z, Li K, Lim YP, Piao Z (2015) Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa. Front Plant Sci 6:432. https://doi.org/10.3389/fpls.2015.00432
Li H, Wang S, Se C, Yang Z, Zhang Q, Xin H, Xu Y, Lin S, Chen X, Yao Z, Yang Q, Fei Z, Huang S, Zhang Z (2022a) Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat Commun 13:682. https://doi.org/10.1038/s41467-022-28362-0
Li W, Liu J, Zhang H, Ze L, Wang Yu, Xing L, He Q (2022b) Plant pan-genomics: recent advances, new challenges and roads ahead. J Genet Genomics 49:833–846
Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C et al (2023a) Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet 55:852–860. https://doi.org/10.1038/s41588-023-01340-y
Li X, Liu W, Wang G, Sun Samuel SM, Yuan L, Wang J (2023b) Improving digestibility of sorghum proteins by CRISPR/Cas9-based genome editing. Food Energy Secur 13:e506. https://doi.org/10.1002/fes3.506
Liang Z, Gupta SK, Cheng-Ting Y, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupta R, Yang J, Varshney RK, Schnable PS, Schnable JC (2018) Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids. G3 8:2513–2522
Liang Z, Wu Y, Ma L, Guo Y, Ran Y (2022) Efficient genome editing in Setaria italica Using CRISPR/Cas9 and base editors. Front Plant Sci 12:815946. https://doi.org/10.3389/fpls.2021.815946
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z (2020) Pan-Genome of wild and cultivated soybeans. Cell 182:162–176. https://doi.org/10.1016/j.cell.2020.05.023
Lopez-Zuniga LO, Wolters P, Davis S, Weldekidan T, Kolkman JM, Nelson R, Hooda KS, Rucker E, Thomason W, Wisser R, Balint-Kurti P (2019) Using maize chromosome segment substitution line populations for the identification of loci associated with multiple disease resistance. G3 9:189–201. https://doi.org/10.1534/g3.118.200866
Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y et al (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun 6:6914. https://doi.org/10.1038/ncomms7914
Lukose CM, Kadvani DL, Dangaria CJ (2007) Efficacy of fungicides in controlling blast disease of pearl millet. Indian Phytopathol 60:68–71
Lye ZN, Purugganan MD (2019) Copy number variation in domestication. Trends Plant Sci 24:352–365. https://doi.org/10.1016/j.tplants.2019.01.003
Mace ES, Cruickshank AW, Tao Y, Hunt CH, Jordan DR (2020) A global resource for exploring and exploiting genetic variation in sorghum crop wild relatives. Crop Sci 61:150–162. https://doi.org/10.1002/csc2.20332
Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63
Mallu TS, Mutinda S, Githiri SM, Achieng Odeny D, Runo S (2021) New pre-attachment Striga resistant sorghum adapted to African agro-ecologies. Pest Manag Sci 77:2894–2902
Mamidi S, Healey A, Huang P et al (2020) A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol 38:1203–1210. https://doi.org/10.1038/s41587-020-0681-2
Mangino G, Arrones A, Plazas M, Pook T, Prohens J, Gramazio P, Vilanova S (2022) Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant. Front Plant Sci 13:847789. https://doi.org/10.3389/fpls.2022.847789
Manning K, Pelling R, Higham T, Schwenninger JL, Fuller DQ (2011) 4500-year old domesticated pearl millet (Pennisetum glaucum) from the Tilemsi valley, Mali: new insights in to an alternative cereal domestication pathway. J Archae Sci 38:312–322
Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gerard B, Ndjeunga J, Bezancon G, Pham JL, Vigouroux Y (2006a) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58. https://doi.org/10.1007/s00122-006-0409-9
Mariac C, Robert T, Allinnee C, Remigereau MS, Luxereau A, Tidjani M, Seyni O, Bezancon G, Pham JL, Sarr A (2006b) Genetic diversity and gene flow among pearl millet crop/weed complex: a case study. Theor Appl Genet 113:1003–1014. https://doi.org/10.1007/s00122-006-0360-9
Marshall VM, Lewis MM, Ostendorf B (2012) Buffel grass (Cenchrus ciliaris) as an invader and threat to biodiversity in arid environments: a review. J Arid Environ 78:1–12. https://doi.org/10.1016/j.jaridenv.2011.11.005
Mathur PN (2012) Global strategy for the ex situ conservation of pearl millet and its wild relatives. Global Crop Diversity Trust, Rome, Italy
Mayer M, Holker AC, González-Segovia E et al (2020) Discovery of beneficial haplotypes for complex traits in maize landraces. Nat Commun 11:4954. https://doi.org/10.1038/s41467-020-18683-3
Mishra S, Singh B, Panda K, Singh BP, Singh N, Misra P, Rai V, Singh NK (2016) Associaton of SNP haplotypes of HKT family genes with salt tolerance in Indian wild rice germplasm. Rice 9:15. https://doi.org/10.1186/s12284-016-0083-8
Muktar MS, Teshome A, Hanson J, Negawo AT, Habte E, Entfellner Jean Baka D, Ki-Won L, Jones CS (2019) Genotyping by sequencing provides new insights in to the diversity of napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between locations. Sci Rep 9:6936. https://doi.org/10.1038/s41598-019-43406-0
Muscolo A, Panuccio MR, Sidari M (2003) Effects of salinity on growth, carbohydrate metabolism and nutritive properties of kikuyugrass (Pennisetum clandestinum Hochst). Plant Sci 164:1103–1110. https://doi.org/10.1016/s0168-9452(03)00119-5
Muscolo A, Panuccio MR, Eshel A (2013) Ecophysiology of Pennisetum clandestinum: a valuable salt tolerant grass. Environ Exp Bot 92:55–63. https://doi.org/10.1016/j.envexpbot.2012.07.009
Mutinda S, Jamil M, Wang JY, Berqdar L, Ateka E, Bellis ES, Al-Babili S, Runo S (2023) Strigolactone biosynthesis lgs1 mutant alleles mined from the sorghum accession panel are a promising resource of resistance to witchweed (Striga) parasitism. Plants People Planet 1–14. https://doi.org/10.1002/ppp3.10442
Nagesh Ch, Subrahmanyam NC (1996) Interspecific hybridization of Pennisetum glaucum (L.) R. Br. with wild relatives. J Plant Biochem Biotechnol 5:1–5. https://doi.org/10.1007/BF03262970
Neelakandan AK, Wright DA, Traore SM, Chen X, Spalding MH, He G (2022) CRISPR/Cas9 based site-specific modification of FAD2 cis-regulatory motifs in peanut (Arachis hypogaea L). Front Genet 13:849961. https://doi.org/10.3389/fgene.2022.849961
Oumar I, Mariac C, Pham JL, Vigouroux Y (2008) Phylogeny and origin of pearl millet [Pennisetum glaucum (L.) R. Br] as revealed by microsatellite loci. Theor Appl Genet 117:489–497
Ousseini IS, Bakasso I, Kane NA, Couderc M, Zekraoui L et al (2017) Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet. Heredity 119:88–94
Pascual L, Desplat N, Huang BE, Desgroux A, Bruguier L, Bouchet JP, Le QH, Chauchard B, Verschave P, Causse M (2015) Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol J 13:565–577. https://doi.org/10.1111/pbi.12282
Passot S, Gnacko F, Moukouanga D, Lucas M, Guyomarc’h S, Moreno Ortega B, Atkinson JA, Belko MN, Bennett MJ, Gantet P, Wells DM, Guedon Y, Vigouroux Y, Verdeil J-L, Muller B, Laplaze L (2016) Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots. Front Plant Sci 7:829. https://doi.org/10.3389/fpls.2016.00829
Patil BD, Hardas MW, Joshi AB (1961) Auto-allopolyploid nature of Pennisetum squamulatum Fresen. Nature 199:419–420
Patil BD, Singh A (1964) An interspecific cross in genus Pennisetum involving two basic numbers. Current Sci 33:255
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556. https://doi.org/10.1038/nature07723
Patil G, Do T, Vuong TD, Valliyodan B, Lee JD, Chaudhary J, Shannon JG, Nguyen HT (2016) Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean. Sci Rep 6:19199. https://doi.org/10.1038/srep19199
Pattanashetti SK, Upadhyaya HD, Dwivedi SL, Vetriventhan M, Reddy KN (2016) Pennisetum. In: Singh M, Upadhyaya HD (eds) Genetic and genomic resources for grain cereals improvement. Academic Press, Elsevier, pp 253–289
Peacock JM, Soman P, Jayachandran R, Rani AU, Howarth CJ, Thomas A (1993) Effect of high soil surface temperature on seedling survival in pearl millet. Exp Agric 29:215–225
Pernes J (1984) Plant genetic resources management, vol 1. ACCT, Paris, France
Perumal R, Tesso TT, Morris GP, Jagadish SVK, Little CR, Bean SR, Yu J, Vara Prasad PV, Tuinstra MR (2021) Registration of the sorghum nested association mapping (NAM) population in RT×430 background. J Plant Regist 15:395–402
Pixley KV, Falck ZJB, Paarlberg RL, Philllips Peter WB, Loedin Inez HS, Dhugga KS, Campos H, Gutterson N (2022) Genome-edited crops for improved food security of smallholder farmers. Nat Genet 54:364–367. https://doi.org/10.1038/s41588-022-01046-7
Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic mapsfor barley and wheat using a novel two-enzymegenotyping-by-sequencing approach. PLoS ONE 7:e32253. https://doi.org/10.1371/journal.pone.0032253
Poncet V, Lamy F, Enjalbert J et al (1998) Genetic analysis of the domestication syndrome in pearl millet (Pennisetum glaucum L., Poaceae): inheritance of the major characters. Heredity 81:648–658. https://doi.org/10.1046/j.1365-2540.1998.00445.x
Poncet V, Lamy F, Devos KM, Gale MD, Sarr A, Robert T (2000) Genetic control of domestication traits in pearl millet (Pennisetum glaucum L., Poaceae). Theor Appl Genet 100:147–159. https://doi.org/10.1007/s001220050020
Poncet V, Martel E, Allouis S, Devos KM, Lamy F, Sarr A, Robert T (2002) Comparative analysis of QTLs affecting domestication traits between two domesticated × wild pearl millet (Pennsietum glaucum L., Poaceae) crosses. Theor Appl Genet 104:965–975
Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Diez MJ, Fita A, Herraiz FJ, Buuruezo AR, Soler S, Knapp S, Vilanova S (2017) Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica 213:158
Qi X, Li MW, Xie M, Liu X, Ni M, Shao G et al (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5:4340. https://doi.org/10.1038/ncomms5340
Rai KN, Appa Rao S, Reddy KN (1997) Pearl millet. In: Fuciillo D, Sears L, Stapleton P (eds) Biodiversity in trust: conservation and use of plant genetic resources in CGIAR centers. Cambridge University Press, pp 243–258
Raj C, Sharma R, Pushpavathi B, Gupta SK, Radhika K (2018) Inheritance and allelic relationship among downy mildew resistance genes in pearl millet. Plant Dis 102:6. https://doi.org/10.1094/PDIS-07-17-0959-RE
Rakotondramanana M, Tanaka R, Tanaka JP, Stangoulis J, Grenier C, Wissuwa M (2022) Genomic prediction of zinc-biofortification potential in rice gene bank accessions. Theor Appl Genet 135:2265–2278
Ramu P, Srivastava RK, Sanyal A et al (2023) Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications. Commun Biol 6:902. https://doi.org/10.1038/s42003-023-05258-3
Rao PP, Birthal PS, Reddy BV, Rai KN, Ramesh S (2006) Diagnostics of sorghum and Harlan pearl millet grains-based nutrition in India. Int Sorghum News Lett 47:93–96
Razzaq A, Kaur P, Akhter N, Wani SH, Saleem F (2021) Next-generation breeding strategies for climate–ready crops. Front Plant Sci 12:620420. https://doi.org/10.3389/fpls.2021.620420
Remigereau MS, Lakis G, Rekima S, Leveugle M, Fontaine MC, Langin T, Sarr A, Robert T (2011) Cereal domestication and evolution of branching: Evidence of soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PLoS ONE 6:e22404. https://doi.org/10.1371/journal.pone.0022404
Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernandez F, Smykal P, Brus J (2022) How could the use of crop wild relatives in breeding increase the adaptation of crops to marginal environments. Front Plant Sci 13:886162. https://doi.org/10.3389/fpls.2022.886162
Robert T, Khalfallah N, Martel E, Lamy F, Poncet V, Allinne C, Remigereau MS, Rekima S, Leveugle M, Lakis G, Yakovlev SS, Sarr A (2011) Pennisetum. In: Kole C (ed) Wild crop relatives: genomic and breeding resources, millets and grasses. Springer-Verlag, Berlin Heidelberg, pp 217–255
Rouamba A, Shimelis H, Drabo I, Mrema E, Ojiewo CO, Mwadzingeni L, Rathore A (2023) Genome-wide association analyses of agronomic traits and striga hermonthica resistance in pearl millet. Sci Rep 13:17152. https://doi.org/10.1038/s41598-023-44046-1
Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H, Edwards D, Deshpande SP, Rathore A (2021) Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain. Front Plant Sci 12:666342. https://doi.org/10.3389/fpls.2021.666342
Salson M, Orjuela J, Mariac C, Zekraoui L, Couderc M, Arribat S, Rodde N, Faye A, Kane NA, Tranchant-Dubreuli C, Vigouroux Y, Berthouly-Salazar C (2023) A strongly improved assembly of the pearl millet reference genome using oxford nanopore long reads and optical mapping. bioRxiv. https://doi.org/10.1101/2023.01.06.522873
Sankar SM, Singh SP, Prakash G, Satyavathi CT, Soumya SL, Yadav Y, Sharma LD, Rao AR, Singh N, Srivastava RK (2021) Deciphering genotype-by-environment interaction for target environmental delineation and identification of stable resistant sources against foliar blast disease of pearl millet. Front Plant Sci 12:656158. https://doi.org/10.3389/fpls.2021.656158
Satyavathi CT, Ambawat S, Khandelwal V, Srivastava RK (2021) Pearl millet: a climate-resilient nutricereal for mitigating hidden hunger and provide nutritional security. Front Plant Sci 12:659938. https://doi.org/10.3389/fpls.2021.659938
Satyavathi CT, Tomar RS, Ambawat S, Kheni J, Padhiyar SM, Desai H, Bhatt SB, Shitap MS, Meena RC, Singhal T, Sankar SM, Singh SP, Khandelwal V (2022) Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]. Sci Rep 12:276. https://doi.org/10.1038/s41598-021-04388-0
Saxena RK, Edwards D, Varshney RK (2014) Structural variations in plant genomes. Brief Funct Genomics 13:296–307. https://doi.org/10.1093/bfgp/elu016
Schank SC, Diz DA, Bates DB, Thomrsola KE (1993) Genetic improvement of napier grass and hybrids with pearl millet. Biomass Bioenerg 5:35–40. https://doi.org/10.1016/0961-9534(93)90005-O
Schmelzer GH (1997) Review of Pennisetum section Brevivalvula (Poaceae). Euphytica 97:1–20. https://doi.org/10.1023/A:1003077906928
Schulthess AW, Kale SM, Liu F, Zhao Y, Philipp N et al (2022) Genomics-informed pre breeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 54:1544–1552. https://doi.org/10.1038/s41588-022-01189-7
Scott MF, Ladejobi O, Amer S, Bentley AR et al (2020) Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity 125:396–416
Sehgal D, Skot L, Singh R, Srivastava RK, Das SP, Taunk J, Sharma PC, Pal R, Raj B, Hash CT, Yadav RS (2015) Exploring potential of pearl millet germplasm association panel for associating mapping of drought tolerance traits. PLoS ONE 10:e0122165. https://doi.org/10.1371/journal.pone.0122165
Selvaraj R, Singh AK, Singh VK et al (2021) Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 11:10082. https://doi.org/10.1038/s41598-021-87964-8
Semalaiyappan J, Selvanayagam S, Rathore A, Gupta SK, Chakraborty A, Gujjula KR, Haktan S, Viswanath A, Malipatil R, Shah P, Govindaraj M, Ignacio JC, Reddy S, Singh AK, Thirunavukkarasu N (2023) Development of AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. Front Plant Sci 13:1068883. https://doi.org/10.3389/fpls.2022.1068883
Serba DD, Muleta KT, St AP, Bernardo A, Bai G, Perumal R, Bashir E (2019) Genetic diversity, population structure and linkage disequilibrium of pearl millet. Plant Genome 12:3. https://doi.org/10.3835/plantgenome2018.11.0091
Serba DD, Yadav RS, Varshney RK, Gupta SK, Mahalingam G, Srivastava RK, Gupta R, Perumal R, Tesso TT (2020). In: Kole C (ed) Genomic designing of pearl millet: a resilient crop for arid and semi-arid environments. Springer Nature, Switzerland, pp 221–286
Shang L, Li X, He H, Yuan Q, Song Y, Wei Z, Lin H, Hu M, Zhao F, Zhang C et al (2022) A super pan-genomic landscape of rice. Cell Res 32:878–896
Sharma S, Upadhyaya HD, Varshney RK, Gowda CLL (2013) Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes. Front Plant Sci 4:309. https://doi.org/10.3389/fpls.2013.00309
Sharma S, Sharma R, Pujar M, Yadav D, Yadav Y, Rathore A, Mahala RS, Singh I, Verma Y, Deora VS, Vaid B, Jayalekha AK, Gupta SK (2020) Use of wild Pennisetum species for improving biotic and abiotic stress tolerance in pearl millet. Crop Sci 61:289–304. https://doi.org/10.1002/csc2.20408
Sharma S, Sharma R, Govindaraj M, Mahala RS, Satyavathi TC, Srivastava RK, Gumma MK, Kilian B (2020a) Harnessing wild relatives of pearl millet for germplasm enhancement: challenges and opportunities. Crop Sci https://doi.org/10.1002/csc2.20343
Sharma S, Sharma R, Pujar M, Yadav D, Yadav Y, Rathore A, Mahala RS, Singh I, Verma Y, Deora VS, Vaid B, Jayalekha AK, Gupta SK (2020b) Use of wild Pennisetum species for improving biotic and abiotic stress tolerance in pearl millet. Crop Sci 61:289–304. https://doi.org/10.1002/csc2.20408
Shi J, Ma X, Zhang J, Zhou Y, Liu M, Huang L et al (2019) Chromosome conformation capture resolved near complete genome assembly of broomcorn millet. Nat Commun 10:464. https://doi.org/10.1038/s41467-018-07876-6
Shi J, Ni X, Huang J, Fu Y, Wang T, Yu H, Zhang Y (2022) CRISPR/Cas9-mediated gene editing of BnFAD2 and BnFAE1 modifies fatty acid profiles in Brassica napus. Genes (basel) 20:1681. https://doi.org/10.3390/genes13101681
Shivhare R, Lata C (2017) Exploration of genetic and genomic resources for abiotic and biotic stress tolerance in pearl millet. Front Plant Sci 7:2069. https://doi.org/10.3389/fpls.2016.02069
Singh SD, Navi SS (2000) Genetic resistance to pearl millet downy mildew II. Resistance in wild relatives. Mycol Plant Pathol 30:167–171
Singh SD, Wilson JP, Navi SS, Talukdar BS, Hess DE, Reddy KN (1997) Screening techniques and sources of resistance to downy mildew and rust in pearl millet. ICRISAT Information Bulletin No. 48, Patancheru, 138pp
Singh K, Kumar S, Raj Kumar S, Singh M, Gupta K (2019) Plant genetic resources management and pre-breeding in genomics era. Indian J Genet 79:117–130. https://doi.org/10.31742/IJGPB.79S.1.1
Sinha P, Singh VK, Saxena RK, Khan AW, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya HD, Kumar A, Varshney RK (2020) Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnol J 18:2482–2490. https://doi.org/10.1111/pbi.13422
Song JL, Wang ZY, Wang YH, Du J, Wang CY, Zhang XQ, Chen S, Huang XL, Xie XM, Zhong TX (2022) Overexpression of Pennisetum purpureum CCoAOMT contributes to lignin deposition and drought tolerance by promoting the accumulation of flavonoids in transgenic tobacco. Front Plant Sci 13:884456
Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y et al (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5:e1000734. https://doi.org/10.1371/journal.pgen.1000734
Srivastava RK, Yadav OP, Kaliamoorthy S, Gupta SK, Serba DD, Choudhary S, Govindaraj M, Kholova J, Murugesan T, Satyavathi CT, Gumma MK, Singh RB, Bollam S, Gupta R, Varshney RK (2022a) Breeding drought-tolerant pearl millet using conventional and genomic approaches: achievements and prospects. Front Plant Sci 13:781524. https://doi.org/10.3389/fpls.2022.781524
Stapf O, Hubbard CE (1934) Pennisetum. In: Prain D (ed) Flora of tropical Africa. Ashford, Kent, UK, Reeve & Co Ltd, pp 954–1070
Stevens CJ, Fuller DQ (2018) Sorghum and pearl millet. In: Lopez Varela SL (ed) The encyclopedia of archaeological sciences. Wiley, Hoboken, pp 1–4
Subudhi PK, Leon T De, Singh PK, Parco A, Cohn MA, Sasaki T (2015) A chromosome segment substitution library of weedy rice for genetic dissection of complex agronomic and domestic traits. PLos One 10: e0130650. https://doi.org/10.1371/journal.pone.0130650
Taunk J, Rani A, Yadav NR, Vartyadav D, Yadav RC, Raj K, Kumar R, Yadav HP (2018) Molecular breeding of ameliorating commercial pearl millet hybrid for downy mildew resistance. J Genet 97:1241–1251
Teng K, Guo Q, Liu L, Guo Y, Xu Y, Hou X, Teng W, Zhang H, Zhao C, Yue Y, Wen H, Wu J, Fan X (2023) Chromosome-level reference genome assembly provides insights in to the evolution of Pennisetum alopecuroides. Front Plant Sci 14:1195479. https://doi.org/10.3389/fpls.2023.1195479
Thakur RP, Rai KN, Khairwal IS, Mahala RS (2008) Strategy for downy mildew resistance breeding in pearl millet in India. SAT eJournal 6:1–11
Tharanya M, Kholova J, Sivasakthi K, Sehgal D, Hash CT, Raj B, Srivastava RK, Baddam R, Thirunalasundari T, Yadav R, Vadez C (2018) Quantitative trait loci (QTLs) for water use and crop production traits co-locate with major QTL for tolerance to water deficit in a fine mapping population of pearl millet (Pennisetum glaucum (L.) R. Br.). Theor Appl Genet 131:1509–1529. https://doi.org/10.1007/s00122-018-3094-6
Timper P, Wilson JP, Johnson AW, Hanna WW (2002) Evaluation of pearl millet grain hybrids for resistance to Meloidogyne spp. and leaf blight caused by Pyricularia grisea. Plant Dis 86:909–914
Torkamaneh D, Laroche J, Valliyodan B, O’Donoughue L, Cober E, Rajcan I, Vilela Abdelnoor R, Sreedasyam A, Schmutz J, Nguyen HT, Belzile F (2021) Soybean (Glycine max) haplotype map (GmHapMap): a universal resource for soybean translational and functional genomics. Plant Biotechnol J 19:324–334. https://doi.org/10.1111/pbi.13466
Upadhyaya HD, Reddy KN, Gowda CLL (2007) Pearl millet germplasm at ICRISAT genebank-Status and impact. J SAT Agri Res 3:1–6
Upadhyaya HD, Reddy KN, Ahmed MI, Kumar V, Gumma MK, Ramachandran S (2017) Geographical distribution of traits and diversity in the world collection of pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] landraces conserved at the ICRISAT gene bank. Genet Resour Crop Evol 64:1365–1381. https://doi.org/10.1007/s10722-016-0442-8
Vadez V, Deshpande SP, Kholová J, Hammer GL, Borrell AK, Talwar HS, Hash CT (2011a) Staygreen QTL effects on water extraction and transpiration efficiency in a lysimetric system: influence of genetic background. Funct Plant Biol 38:553–566
Vadez V, Krishnamurthy L, Hash CT, Upadhyaya HD, Borrell AK (2011b) Yield, transpiration efficiency, and water use variations and their relationships in the sorghum reference collection. Crop Pasture Sci 62:1–11
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J et al (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 35:969–976. https://doi.org/10.1038/nbt.3943
Varshney RK, Singh VK, Kumar A, Powell W, Sorrells ME (2018) Can genomes deliver climate change ready crops? Curr Opin Plant Biol 45:205–211. https://doi.org/10.1016/j.pbi.2018.03.007
Varshney RK, Pandey MK, Bohra A, Singh VK, Thudi M, Saxena RK (2019) Toward the sequence based breeding in legumes in the post-genome sequencing era. Theor Appl Genet 132:797–816
Varshney RK, Roorkiwal M, Sun S et al (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 599:622–627. https://doi.org/10.1038/s41586-021-04066-1
Wang YX, Xiong GS, Hu J, Jiang L, Yu H, Xu J, Fang YX, Zeng LJ, Xu EB, Xu J et al (2015) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–948
Wang W, Mauleon R, Hu Z et al (2018a) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557:43–49. https://doi.org/10.1038/s41586-018-0063-9
Wang Y, Zhang X, Shi X, Sun C, Jin J, Tian R, Wei X, Xie H, Guo Z, Tang J (2018b) Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations. Sci Rep 8:11101. https://doi.org/10.1038/s41598-018-29338-1
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF (2021) Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 39:1348–1365. https://doi.org/10.1038/s41587-021-01108-x
Wang S, Qian YQ, Zhao RP, Chen LL, Song JM (2023) Graph-based pan-genomes: increased opportunities in plant genomics. J Exp Bot 74:24–39. https://doi.org/10.1093/jxb/erac412
Wilson JP, Gates RN (1993) Forage yield losses in hybrid pearlmillet due to leaf blight caused primarily by Pyricularia grisea. Phytopathology 83:739–743
Wilson JP, Hanna WW (1992) Disease resistance in wild Pennisetum species. Plant Dis 76:1171–1175
Wilson JP, Hanna WW, Gascho G, Wilson DM (1995) Pearl millet grain yield loss from rust infection. In: Teare ID (ed) Proceedings of the first national grain pearl millet symposium. University of Georgia, Tifton, GA, USA, pp 54–56
Wilson JP, Hanna WW, Gascho GJ (1996) Pearl millet grain yield loss from rust infection. J Prod Agric 9:543–545. https://doi.org/10.2134/jpa1996.0543
Wilson JP, Hess DE, Hanna WW (2000) Resistance to Striga hermonthica in wild accessions of the primary gene pool of Pennisetum glaucum. Phytopathology 90:1169–1172. https://doi.org/10.1094/PHYTO.2000.90.10.1169
Wilson JP, Hess DE, Hanna WW, Kumar KA, Gupta SC (2004) Pennisetum glaucum subsp. monodii accessions with striga resistance in West Africa. Crop Prot 23:865–870. https://doi.org/10.1016/j.cropro.2004.01.006
Winkel T, Renno JF, Payne W (1997) Effect of the timing of water deficit on growth, phenology and yield of pearl millet (Pennisetum glaucum (L.) R. Br.) grown in Sahelian conditions. J Exp Bot 48:1001–1009. https://doi.org/10.1093/jxb/48.5.1001
Xu J, Liu C, Li M (2021) Comparactive analysis of the chloroplast genome for four pennisetum species: Molecular structure and phylogenetic relationships. Front Genet 12:687844. https://doi.org/10.3389/fgene.2021.687844
Yadav R, Hash C, Bidinger F, Cavan G, Howarth C (2002) Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions. Theor Appl Genet 104:67–83. https://doi.org/10.1007/s001220200008
Yadav OP, Gupta SK, Govindaraj M, Sharma R, Varshney RK, Srivastava RK, Rathore A, Mahala RS (2021) Genetic gains in pearl millet in India: insights into historic breeding strategies and future perspective. Front Plant Sci 12:645038. https://doi.org/10.3389/fpls.2021.645038
Yan Q, Wu F, Xu P, Sun Z, Li J, Gao L, Lu L, Chen D, Muktar M, Jones C, Yi X, Zhang J (2021) The elephant grass (Pennisetum purpureus) genome provides insights in to anthocyanidin accumulation and fast growth. Mol Ecol Resour 21:526–542. https://doi.org/10.1111/1755-0998.13271
Yan H, Sun M, Zhang Z et al (2023) Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 55:1–12. https://doi.org/10.1038/s41588-023-01302-4
Yu X, Li X, Guo T, Zhu C, Wu Y, Mitchell SE, Roozeboom KL, Wang D, Wang ML, Pederson GA, Tesso TT, Schnable PS, Bernardo R, Yu J (2016a) Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nat Plants 2:16150. https://doi.org/10.1038/NPLANTS.2016.150
Yuan R, Zhao N, Usman B, Luo L, Liao S, Qin Y, Nawaz G, Li R (2020) Development of chromosome segment substitution lines (CSSLs) derived from Guangxi wild rice (Oryza rufipogon Griff.) under rice (Oryza sativa L.) background and the identification of QTLs for plant architecture, agronomic traits and cold tolerance. Genes 11:980. https://doi.org/10.3390/genes11090980
Zaw H, Raghavan C, Pocsedio A, Swamy BPM, Jubay ML, Singh RK, Bonifacio J, Mauleon R, Hernandez JE, Mendioro MS, Gregorio GB, Leung H (2019) Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population. Sci Rep 9:19605. https://doi.org/10.1038/s41598-019-55357-7
Zhang H, Mittal N, Leamy NJ, Barazani O, Song BH (2016) Back in to the wild-apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 10:5–24. https://doi.org/10.1111/eva.12434
Zhang W, Zhang S, Lu X, Can Li, Liu X, Dong G, Xia T (2020) Tissue-specific transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum). BMC Plant Biol 20:528. https://doi.org/10.1186/s12870-020-02735-3
Zhang A, Ji Y, Sun M, Lin C, Zhou P, Ren J, Luo D, Wang X, Ma C, Zhang X, Feng G, Nie G, Huang L (2021a) Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage. BMC Genomics 22:568. https://doi.org/10.1186/s12864-021-07888-5
Zhang L, Liu D, Ma Y, Yang S, Wang X, Wang Y, Dong R (2021b) The complete chloroplast genome sequence of Pennisetum centrasiaticum, a widespread grass in Tibet, China. Mitochondrial DNA B 6:2105–2106. https://doi.org/10.1080/23802359.2021.1903355
Zhang Z, Guo J, Cai X, Li Y, Xi X, Lin R, Liang J, Wang X, Wu J (2022) Improved reference genome annotation of Brassica rapa by pacific biosciences RNA sequencing. Front Plant Sci 13:841618. https://doi.org/10.3389/fpls.2022.841618
Zheng H, Wang B, Hua X, Gao R, Wang Y, Zhang Z, Zhang Y, Mei J, Huang Y, Huang Y, Lin H, Zhang X, Lin D, Lan S, Liu Z, Liu Z, Lu G, Wang Z, Ming R, Zhang J, Lin Z (2023) A near complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights in to its evolution and C4 photosynthesis. Plant Commun. https://doi.org/10.1016/j.xplc.2023.100633
Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y et al (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33:408–414. https://doi.org/10.1038/nbt.3096
Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR et al (2017) Exploring structural variation and gene family architecture with de Novo assemblies of 15 Medicago genomes. BMC Genom 18:261. https://doi.org/10.1186/s12864-017-3654-1
Zhou SF, Wang CR, Frazier TP et al (2018) The first Illumina-based de novo transcriptome analysis and molecular marker development in Napier grass (Pennisetum purpureum) Mol Breed 38:95–108. https://doi.org/10.1007/s11032-018-0852-8
Zhu W, Lin J, Yang D, Zhao L, Zhang Y, Zhu Z, Chen T, Wang C (2009) Development of chromosome segment substitution lines derived from backcross between two sequenced rice cultivars, Indica recipient 93–11 and Japonica donor Nipponbare. Plant Mol Bio Rep 27:126–131. https://doi.org/10.1007/s11105-008-0054-3
Acknowledgements
The authors express sincere gratitude to The Director ICAR-IARI for providing necessary facilities to carry out the study.
Funding
No funding was received for conducting the study.
Author information
Authors and Affiliations
Contributions
CK conceived the idea of manuscript; CK, MS, A drafted the manuscript; SP, NS and SK reviewed and edited the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Communicated by Dorothea Bartels.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Kapoor, C., Anamika, Mukesh Sankar, S. et al. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. Planta 259, 155 (2024). https://doi.org/10.1007/s00425-024-04423-0
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00425-024-04423-0