Abstract
Grain yield is a quantitative trait, which is determined by several agronomic traits. Unfortunately, there is little information about the genetics behind yield components in US rice cultivars. The objectives of the present study were to (1) conduct a QTL study to identify chromosome (chr. hereafter) regions associated with yield traits in two U.S.-developed rice cultivars and (2) identify candidate genes in major QTL regions related to yield traits. Four rice cultivars were evaluated in summer 2017 at the University of Arkansas System Division of Agriculture's Rice Research and Extension Center (RREC) at Stuttgart, AR. for 15 agronomic traits associated with yield. Of the four cultivars, "LaGrue" had a higher number of seeds/panicle, number of primary panicle branches/panicle, and number of seeds/plant and "Lemont," despite having longer panicles and higher 100 seed weight/panicle, produced the least number of seeds among the cultivars. A bi-parental population was developed from a cross between LaGrue and Lemont for QTL analysis. A set of 322 F2:3 lines were evaluated in a randomized complete block design (RCBD) for several agronomic traits at two locations with three replications for each line. A total of 17 major QTL were detected, including two major QTL for plant height on chr. 1 and two major QTL for flag leaf length and panicle length on chr. 8 with seven candidate genes found in these regions. The results from the study would be useful for marker-assisted selection in rice breeding.
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Abbreviations
- DTHDT:
-
Days to 50% heading
- FLLT:
-
Flag leaf length
- FWD:
-
Flag leaf width
- PBN:
-
Primary branch number
- PlntHt:
-
Plant height
- PnL:
-
Panicle length
- SBN:
-
Secondary branch number
- Sp/Pl:
-
Number of spikelets/panicle
- Sd/Pl:
-
Number of seeds/panicle
- chr.:
-
Chromosome
- cM:
-
CentiMorgan
References
Begum H, Spindel JE, Lalusin A, BorromeoT GG, Hernandez J et al (2015) Genome-wide association mapping for yield and other agronomictraits in an elite breeding population of tropical rice (Oryza sativa). PLoS ONE 10(3):e0119873. https://doi.org/10.1371/journal.pone.0119873
Bollich CN, Webb BD, Marchetti MA, Scott JE (1985) Registration of ‘Lemont’ rice. Crop Sci 25(5):883–885
Cheng FM, Zhang QF, Zhu HJ, Zhao NC, Wang F, Chen KM, Zhang GP (2007) The difference in amylose content within a panicle as affected by the panicle morphology of rice cultivars. J Cereal Sci 46(1):49–57
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142(1):169–196. https://doi.org/10.1007/s10681-005-1681-5
Cui R, Han J, Zhao S, Su K, Wu F, Du X et al (2010) Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). Plant J 61(5):767–781. https://doi.org/10.1111/j.1365-313X.2009.04101.x
Devi KR, Chandra BS, Lingaiah N, Hari Y, Venkanna V (2017) Analysis of variability, correlation and path coefficient studies for yield and quality traits in rice (Oryza sativa L.). Agric Sci Digest-A Res J 37(1):1–9
Han Z, Hu W, Tan C, Xing Y (2017) QTLs for days to heading and plant height under multiple environments in rice. Genetica 145(1):67–77. https://doi.org/10.1007/s10709-016-9946-6
Hardke J (2018) Introduction. In: Hardke J, Goforth L (eds) Rice production handbook. University of Arkansas Cooperative Extension Service Center Print Media, Little Rock, Arkansas, pp 1–9
Hardke J (2019) Rice Production in Arkansas. University of Arkansas Division of Agriculture Research and Extension. https://www.uaex.edu/farm-ranch/crops-commercial-horticulture/rice/
Hittalmani S, Shashidhar HE, Bagali PG, Huang N, Sidhu JS, Singh VP, Khush GS (2002) Molecular mapping of quantitative trait loci for plant growth, yield and yield related traits across three diverse locations in a doubled haploid rice population. Euphytica 125(2):207–214. https://doi.org/10.1023/A:1015890125247
Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang J et al (2003) Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107(4):679–690. https://doi.org/10.1007/s00122-003-1269-1
Huang K, Wang D, Duan P, Zhang B, Xu R, L, N, Li Y, (2017) WIDE AND THICK GRAIN 1, which encodes an otubain-like protease with deubiquitination activity, influences grain size and shape in rice. Plant J 91(5):849–860. https://doi.org/10.1111/tpj.13613
International Rice Research Institute (1967) Annual report for 1966, pp 59–82
Johnston TH, Wells BR, Marchetti MA, Lee FN, Henry SE (1979) Registration of ‘Mars’ Rice1. Crop Sci 19(5):743. https://doi.org/10.2135/cropsci1979.0011183X001900050058x
Kosambi DD (2016) The estimation of map distances from recombination values. In: Ramaswamy R (ed) Springer, New Delhi, pp 125–130. https://doi.org/10.1007/978-81-322-3676-4_16
Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140(1):12–17. https://doi.org/10.1104/pp.105.063008
Ke S, Liu X, Luan X, Yang W, Zhu H, Liu G et al (2018) Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.). Gene 675:285–300. https://doi.org/10.1016/j.gene.2018.06.105
Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S et al (2003) QTL × environment interactions in rice. I. Days to heading and plant height. Theor Appl Genet 108(1):141–153. https://doi.org/10.1007/s00122-003-1401-2
Linscombe SD, Jodari F, McKenzie KS, Bollich PK, White LM, Groth DE, Dunand RT (1993) Registration of “Bengal” rice. Crop Sci 33(3):645. https://doi.org/10.2135/cropsci1993.0011183X003300030046x
Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR, Tai TH (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45(1):66–76. https://doi.org/10.2135/cropsci2005.0066
McClung AM, Edwards JD, Jia MH, Huggins TD, Bockelman HE, Ali ML, Eizenga GC (2020) Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA−ARS rice collection. Crop Sci 60(6):3191–3211
Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB et al (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107(1):89–101. https://doi.org/10.1007/s00122-003-1192-5
Mei HW, Li ZK, Shu QY, Guo LB, Wang YP, Yu XQ et al (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110(4):649–659. https://doi.org/10.1007/s00122-004-1890-7
Meng L, Li H, Zhang L, Wang J (2015) QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3(3):269–283. https://doi.org/10.1016/j.cj.2015.01.001
Miura K, Ikeda M, Matsubara A, Song X, Ito M, Asano K et al (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42(6):545–549
Miura K, Ashikari M, Matsuoka M (2011) The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci 16(6):319–326
Moldenhauer KAK, Gravois KA, Lee FN, Norman RJ, Bernhardt JL, Wells BR, Blocker MM (1994) Registration of ‘LaGrue’rice. Crop Sci 34(4):1123–1124
Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y et al (2002) Positional cloning of rice semidwarfing gene, sd-1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9(1):11–17
Morales KY, Singh N, Perez FA, Ignacio JC, Thapa R, Arbelaez JD, Tabien RE et al (2020) An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies. PloS One 15(5):e0232479. https://doi.org/10.1371/journal.pone.0232479
Peng Y, Gao Z, Zhang B, Liu C, Xu J, Ruan B et al (2014) Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice. Plant Cell Rep 33(11):1843–1850. https://doi.org/10.1007/s00299-014-1661-0
Rice productivity (2019) Ricepedia. http://ricepedia.org/rice-as-a-crop/rice-productivity
Samonte SOP, Samonte SOP, Wilson LT, Wilson LT, McClung AM (1998) Path analyses of yield and yield-related traits of fifteen diverse rice genotypes. Crop Sci 38(5):1130–1136. https://doi.org/10.2135/cropsci1998.0011183X003800050004x
Sasahara H, Fukuta Y, Fukuyama T (1999) Mapping of QTLs for vascular bundle system and spike morphology in rice, Oryza sativa L. Breed Sci 49:75–81
Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D et al (2002) A mutant gibberellin-synthesis gene in rice. Nature 416(6882):701–702. https://doi.org/10.1038/416701a
Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O rufipogon. Theor Appl Genet 107(8):1419–1432. https://doi.org/10.1007/s00122-003-1373-2
Shang F, Chen L, Meng X, Yang K, Wang J (2020) Fine mapping and grain yield analysis of a major QTL controlling primary branch number in rice (Oryza sativa L.). Genet Resour Crop Evol 67(2):421–431. https://doi.org/10.1007/s10722-019-00857-8
Sharma A, McClung A, Pinson S, Kepiro J, Shank A, Tabien R, Fjellstrom R (2009) Genetic mapping of sheath blight resistance QTLs within Tropical japonica rice cultivars. Crop Sci 49:256–264. https://doi.org/10.2135/cropsci2008.03.0124
Subudhi P, Leon T, Singh P, Parco A, Cohn M, Sasaki T (2015) A chromosome segment substitution library of weedy rice for genetic dissection of complex agronomic and domestication traits. PLoS ONE 10(6):e0130650. https://doi.org/10.1371/journal.pone.0130650
Sun Z, Yin X, Ding J, Yu D, Hu M, Sun X et al (2017) QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza sativa cultivars HR1128 and ’nipponbare. PLoS ONE 12(4):e0175692. https://doi.org/10.1371/journal.pone.0175692
Thomson MJ, Tai TH, McClung AM, Lai X, Hinga ME, Lobos KB et al (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107(3):479–493. https://doi.org/10.1007/s00122-003-1270-8
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X et al (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44(8):950–954. https://doi.org/10.1038/ng.2327
Wang J, Lo S, Li Y, Chen P, Lin S, Ho T et al (2013) Ectopic expression of OsMADS45 activates the upstream genes Hd3a and RFT1 at an early development stage causing early flowering in rice. Bot Stud 54(1):1–13. https://doi.org/10.1186/1999-3110-54-12
Wang S, Li S, Liu Q, Wu K, Zhang J, Wang S et al (2015) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet 47(8):949–954. https://doi.org/10.1038/ng.3352
Wang S, Wu K, Qian Q, Liu Q, Li Q, Pan Y et al (2017) Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Res 27(9):1142–1156. https://doi.org/10.1038/cr.2017.98
Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M et al (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci USA 111(10):3877–3882. https://doi.org/10.1073/pnas.1318131111
Wu W, Zhang Y, Zhang M, Zhan X, Shen X, Yu P et al (2018) The rice CONSTANS-like protein OsCOL15 suppresses flowering by promoting Ghd7 and repressing RID1. Biochem Biophys Res Commun 495(1):1349–1355. https://doi.org/10.1016/j.bbrc.2017.11.095
Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61(1):421–442. https://doi.org/10.1146/annurev-arplant-042809-112209
Yamagishi J, Miyamoto N, Hirotsu S, Laza RC, Nemoto K (2004) QTLs for branching, floret formation, and pre-flowering floret abortion of rice panicle in a temperate japonica × tropical japonica cross. Theor Appl Genet 109:1555–1561. https://doi.org/10.1007/s00122-004-1795-5
Yamagishi M, Takeuchi Y, Kono I, Yano M (2001) QTL analysis for panicle characteristics in Temperate Japonica rice. Euphytica 128:219–224
Zhang L, Wang J, Wang J, Wang L, Ma B, Zeng L et al (2015) Quantitative trait locus analysis and fine mapping of the qPL6 locus for panicle length in rice. Theor Appl Genet 128(6):1151–1161. https://doi.org/10.1007/s00122-015-2496-y
Zhang P, Zhong K, Zhong Z, Tong H (2019) Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.). BMC Plant Biol 19(1):259–259. https://doi.org/10.1186/s12870-019-1842-7
Zhu J, Zhu J, Zhou Y, Zhou Y, Liu Y, Liu Y, Liang G (2011) Fine mapping of a major QTL controlling panicle number in rice. Mol Breed 27(2):171–180. https://doi.org/10.1007/s11032-010-9420-6
Acknowledgements
This work was supported in part by funding provided by the rice farmers of Arkansas and administered by the Arkansas Rice Research and Promotion Board. We thank Mr. Thomas Colman and Mr. Daniel Wood for their help.
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Rice, A.D., North, D.G., Moldenhauer, K.A.K. et al. QTL mapping of panicle architecture and yield-related traits between two US rice cultivars 'LaGrue' and 'Lemont'. Euphytica 218, 7 (2022). https://doi.org/10.1007/s10681-021-02940-7
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DOI: https://doi.org/10.1007/s10681-021-02940-7