Abstract
A starting point to understanding more about underutilised and orphan crops is to investigate their genetic diversity and origins. Whilst whole genome analyses will give a wealth of information in this regard, this is often impractical in terms of cost and an overkill in terms of these initial goals. Therefore, molecular markers are used to establish the partitioning of genetic variation, the location of domestication, and relationships between these crops and their wild relatives. All of this will generate information required to begin improving these crops and identify adaptive variation. A convenient and high throughput way to generate molecular marker information is to mine a genome for markers such as Simple Sequence Repeat markers (SSRs) or others. In this analysis we assembled draft genomes for three underutilised crops (slender Amaranth [Amaranthus viridis L.], lychee [Litchi chinensis Sonn.] and velvet bean [Mucuna pruriens (L.) DC.]) using publicly available data. We show that whilst the assembly could be improved considerably in terms of completeness and duplication, this can house thousands of potential SSR markers. In addition, the chloroplast DNA (cpDNA) was assembled from the same sequencing reads and housed ca. 50–60 potential SSR markers. We also identified 10–11 million potential SNP markers by comparing three genomes for lychee. The approach we use relies solely on publicly available software and can be modified or adapted by others with ease.
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References
Asseng S, Ewert F, Martre P, Rotter RP, Lobell DB, Cammarano D et al (2015) Rising temperatures reduce global wheat production. Nat Clim Chang 5(2):143–147. https://doi.org/10.1038/nclimate2470
Basu S, Roberts JA, Azam-Ali SN, Mayes S (2007) Development of microsatellite markers for bambara groundnut (Vigna subterranea L. Verdc.)—an underutilized African legume crop species. Mol Ecol Notes 7(6):1326–1328. https://doi.org/10.1111/j.1471-8286.2007.01870.x
Bolger A, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Buckles D (1995) Velvetbean: a “new” plant with a history. Econ Bot 49(1):13–25. https://doi.org/10.1007/BF02862271
Burger JC, Chapman MA, Burke JM (2008) Molecular insights into the evolution of crop plants. Am J Bot 95:113–122
Burke JM, Burger JC, Chapman MA (2007) Crop evolution: from genetics to genomics. Curr Opin Genet Dev 17(6):525–532
Campbell BM, Vermeulen SJ, Aggarwal PK, Corner-Dolloff C, Girvetz E, Loboguerrero AM et al (2016) Reducing risks to food security from climate change. Glob Food Sec 11:34–43. https://doi.org/10.1016/j.gfs.2016.06.002
Chapman MA (2015) Transcriptome sequencing and marker development for four underutilized legumes. Appl Plant Sci 3(2):1400111
Chapman MA (2019) Optimizing depth and type of high-throughput sequencing data for microsatellite discovery. Appl Plant Sci 7(11):e11298. https://doi.org/10.1002/aps3.11298
Chapman MA, Hvala J, Strever J, Matvienko M, Kozik A, Michelmore RW et al (2009) Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet 120(1):85–91. https://doi.org/10.1007/s00122-009-1161-8
Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in Eukaryotes. Nature 371(6494):215–220
Dachapak S, Somta P, Poonchaivilaisak S, Yimram T, Srinives P (2017) Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis. Genetica 145(2):189–200. https://doi.org/10.1007/s10709-017-9957-y
De Bellis F, Malapa R, Kagy V, Lebegin S, Billot C, Labouisse JP (2016) New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing. Appl Plant Sci 4(8). https://doi.org/10.3732/apps.1600021
Deletre M, Soengas B, Utge J, Lambourdiere J, Sorensen M (2013) Microsatellite markers for the yam bean Pachyrhizus (Fabaceae). Appl Plant Sci 1(7). https://doi.org/10.3732/apps.1200551
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(3):1070–1082. https://doi.org/10.2135/cropsci2016.10.0885
Dierckxsens N, Mardulyn P, Smits G (2016) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res45(4):e18-e. https://doi.org/10.1093/nar/gkw955
Dixit A, Chung JW, Zhao WG, Lee GA, Lee DH, Ma KH et al (2010) Development of new microsatellite markers for molecular diversity analysis of Citrus species. J Hortic Sci Biotechnol 85(6):521–527. https://doi.org/10.1080/14620316.2010.11512708
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127(7):1309–1321
Doganlar S, Frary A, Daunay MC, Lester RN, Tanksley SD (2002) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161(4):1713–1726
Ekué MR, Gailing O, Finkeldey R (2009) Transferability of Simple Sequence Repeat (SSR) markers developed in Litchi chinensis to Blighia sapida (Sapindaceae). Plant Mol Biol Report 27(4):570–574. https://doi.org/10.1007/s11105-009-0115-2
Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132
Ge L, Yu J, Wang H, Luth D, Bai G, Wang K et al (2016) Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proc Natl Acad Sci 113(44):12414–12419. https://doi.org/10.1073/pnas.1611763113
Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF et al (2010) Food security: the challenge of feeding 9 billion people. Science 327(5967):812–818. https://doi.org/10.1126/science.1185383
Greiner S, Lehwark P, Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47(W1):W59–W64. https://doi.org/10.1093/nar/gkz238
Haq N (1983) New food legume crops for the tropics. Ciba Found Symp 97:144–160
Hawkes JG (1991) 1. The importance of genetic resources in plant breeding. Biol J Linn Soc 43(1):3–10. https://doi.org/10.1111/j.1095-8312.1991.tb00578.x
Hodel RGJ, Gitzendanner MA, Germain-Aubrey CC, Liu XX, Crowl AA, Sun M et al (2016) A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes. Appl Plant Sci 4(6):1600024. https://doi.org/10.3732/apps.1600024
Kauffman CS (1992) Realizing the potential of grain amaranth. Food Rev Int 8(1):5–21. https://doi.org/10.1080/87559129209540927
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923
Li C, Lin F, An D, Wang W, Huang R (2017) Genome sequencing and assembly by long reads in plants. Genes 9(1):6. https://doi.org/10.3390/genes9010006
Li C, Wang Y, Huang X, Li J, Wang H, Li J (2013) De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. BMC Genomics 14(1):552. https://doi.org/10.1186/1471-2164-14-552
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al (2009) The sequence alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Li X, Yadav R, Siddique KHM (2020) Neglected and underutilized crop species: the key to improving dietary diversity and fighting hunger and malnutrition in Asia and the Pacific. Front Nutr 7:593711. https://doi.org/10.3389/fnut.2020.593711
Lin Z, Li X, Shannon LM, Yeh C-T, Wang ML, Bai G et al (2012) Parallel domestication of the Shattering1 genes in cereals. Nat Genet 44(6):720–724. https://doi.org/10.1038/ng.2281
Liu B, Watanabe S, Uchiyama T, Kong F, Kanazawa A, Xia Z et al (2010) The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol 153(1):198–210. https://doi.org/10.1104/pp.109.150607
Liu H, Wei J, Yang T, Mu W, Song B, Yang T et al (2019) Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden. GigaScience 8(4):giz007. https://doi.org/10.1093/gigascience/giz007
Liu W, Xiao Z, Bao X, Yang X, Fang J, Xiang X (2015) Identifying Litchi (Litchi chinensis Sonn.) Cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers. Plos One 10(8):e0135390. https://doi.org/10.1371/journal.pone.0135390
Menzel C (2002) the lychee crop in Asia and the Pacific. Bangkok, Thailand: FAO Regional Office for Asia and the Pacific
Meyer RS, Purugganan MD (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14(12):840–852
Mickelbart MV, Hasegawa PM, Bailey-Serres J (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 16(4):237–251. https://doi.org/10.1038/nrg3901
National Research Council (2006) Lost crops of Africa: volume II: vegetables. The National Academies Press,Washington, DC
NAS (1975) Underexploited tropical plants with promising economic value. National Academy of Sciences, Washington, D.C., USA
Rai N, Kumar S, Singh RK, Rai K, Tiwari G, Kashyap SP et al (2016) Genetic diversity in Indian bean (Lablab purpureus) accessions as revealed by quantitative traits and cross-species transferable SSR markers. Indian J Agric Sci 86:1193–1200
Repinski SL, Kwak M, Gepts P (2012) The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor Appl Genet 124(8):1539–1547. https://doi.org/10.1007/s00122-012-1808-8
Robotham O, Chapman MA (2015) Population genetic analysis of hyacinth bean (Lablab purpureus (L.) Sweet, Leguminosae) indicates an East African origin and variation in drought tolerance. Genet Resour Crop Evol 64:139–148
Sathyanarayana N, Pittala RK, Tripathi PK, Chopra R, Singh HR, Belamkar V et al (2017) Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics 18:409. https://doi.org/10.1186/s12864-017-3780-9
Saxena RK, Prathima C, Saxena KB, Hoisington DA, Singh NK, Varshney RK (2010) Novel SSR Markers for Polymorphism Detection in Pigeonpea (Cajanus spp.). Plant Breed 129(2):142–148. https://doi.org/10.1111/j.1439-0523.2009.01680.x
Sharma V, Rana M, Katoch M, Sharma PK, Ghani M, Rana JC et al (2015) Development of SSR and ILP markers in horsegram (Macrotyloma uniflorum), their characterization, cross-transferability and relevance for mapping. Mol Breed 35(4):102. https://doi.org/10.1007/s11032-015-0297-2
Shrivastava A, Kumar A, Thomas JD, Laserson KF, Bhushan G, Carter MD et al (2017) Association of acute toxic encephalopathy with litchi consumption in an outbreak in Muzaffarpur, India, 2014: a case-control study. Lancet Glob Health 5(4):e458–e466. https://doi.org/10.1016/S2214-109X(17)30035-9
Siddique KHM, Li X, Gruber K (2021) Rediscovering Asia’s forgotten crops to fight chronic and hidden hunger. Nat Plants. 7(2):116–122. https://doi.org/10.1038/s41477-021-00850-z
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117–1123. https://doi.org/10.1101/gr.089532.108
Somta P, Chankaew S, Rungnoi O, Srinives P (2011) Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers. Genome54(11):898–910. https://doi.org/10.1139/g11-056
Takahashi Y, Somta P, Muto C, Iseki K, Naito K, Pandiyan M et al (2016) Novel genetic resources in the genus Vigna unveiled from gene bank accessions. Plos One 11(1):e0147568. https://doi.org/10.1371/journal.pone.0147568
Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W et al (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 9:137
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422
Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P et al (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 47(21):10994–11006. https://doi.org/10.1093/nar/gkz841
Varshney RK, Dubey A (2009) Novel genomic tools and modern genetic and breeding approaches for crop improvement. J Plant Biochem Biotechnol 18(2):127–138
Viruel MA, Hormaza JI (2004) Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae). Theor Appl Genet 108(5):896–902. https://doi.org/10.1007/s00122-003-1497-4
Waselkov KE, Boleda A, Olsen K (2018) A Phylogeny of the genus Amaranthus (Amaranthaceae) based on several low-copy nuclear loci and chloroplast regions. Syst Bot 43:439–458
Williams JT, Haq N (2000) Global research on underutilized crops. An assessment of current activities and proposals for enhanced cooperation
Wong QN, Tanzi AS, Ho WK, Malla S, Blythe M, Karunaratne A et al (2017) Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment. Genes 8(3). https://doi.org/10.3390/genes8030100
Yang S, Grall A, Chapman MA (2018) Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.; Fabaceae) a multi-purpose underutilised legume. Am J Bot 105:888–897
Zeven AC, de Wet JMJ (1982) Dictionary of cultivated plants and their regions of diversity, 2nd edn. Centre for Agricultural Publishing and Documentation, Wageningen, Netherlands
Zhao C, Liu B, Piao S, Wang X, Lobell DB, Huang Y et al (2017) Temperature increase reduces global yields of major crops in four independent estimates. Proc Natl Acad Sci USA 114(35):9326–9331.https://doi.org/10.1073/pnas.1701762114
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Chapman, M.A., Fisher, D. (2022). Utilising Public Resources for Fundamental Work in Underutilised and Orphan Crops. In: Chapman, M.A. (eds) Underutilised Crop Genomes . Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-031-00848-1_24
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