Genome‐Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

Plant Genome - Tập 9 Số 2 - 2016
Richard Boyles1, Elizabeth Cooper2, Matthew T. Myers2, Zachary Brenton1, B. Rauh2, Geoffrey P. Morris3, Stephen Kresovich2,1
1Dep. of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, 29634
2Advanced Plant Technology Program, Clemson University, Clemson, South Carolina, 29634
3Dep. of Agronomy, Kansas State University, Manhattan, Kansas, 66506

Tóm tắt

Grain yield and its primary determinants, grain number and weight, are important traits in cereal crops that have been well studied; however, the genetic basis of and interactions between these traits remain poorly understood. Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000‐grain weight (TGW) in sorghum [Sorghum bicolor (L.) Moench], a hardy C4 cereal with a genome size of ∼730 Mb, was implemented in a diversity panel containing 390 accessions. These accessions were genotyped to obtain 268,830 single‐nucleotide polymorphisms (SNPs). Genome‐wide association studies (GWAS) were performed to identify loci associated with each grain yield component and understand the genetic interactions between these traits. Genome‐wide association studies identified associations across the genome with YPP, GNP, and TGW that were located within previously mapped sorghum QTL for panicle weight, grain yield, and seed size, respectively. There were no significant associations between GNP and TGW that were within 100 kb, much greater than the average linkage disequilibrium (LD) in sorghum. The identification of nonoverlapping loci for grain number and weight suggests these traits may be manipulated independently to increase the grain yield of sorghum. Following GWAS, genomic regions surrounding each associated SNP were mined for candidate genes. Previously published expression data indicated several TGW candidate genes, including an ethylene receptor homolog, were primarily expressed within developing seed tissues to support GWAS. Furthermore, maize (Zea mays L.) homologs of identified TGW candidates were differentially expressed within the seed between small‐ and large‐kernel lines from a segregating maize population.

Từ khóa


Tài liệu tham khảo

10.1534/g3.114.016394

10.1016/j.fcr.2014.11.014

10.2135/cropsci1998.0011183X003800050029x

10.18637/jss.v067.i01

10.1371/journal.pone.0119873

Borrell A.K., 1999, Stay‐green trait associated with yield in recombinant inbred sorghum lines varying in rate of leaf senescence, Int. Sorg. Mill. Newsl., 40, 31

10.1371/journal.pone.0033470

10.1007/s00122‐006‐0352‐9

10.1534/genetics.108.092239

10.2135/cropsci2007.02.0080

10.1007/s11103‐010‐9686‐4

10.1104/pp.108.131227

10.4161/fly.19695

10.2135/cropsci2003.8240

10.1073/pnas.1010179107

10.1086/675497

10.2135/cropsci1967.0011183X000700030035x

Dahlberg J., 2011, Assessing sorghum [Sorghum bicolor (L.) Moench] germplasm for new traits: Food, fuels and unique uses, Maydica, 56, 85

10.1093/bioinformatics/btr330

10.1111/j.1365‐313X.2012.05005.x

10.1186/1471‐2164‐12‐514

10.5923/j.scit.20120202.03

FAO, 2015, FAOSTAT Statistics Database

10.1007/s00122‐006‐0232‐3

10.1186/1471‐2229‐10‐63

10.1071/CP11051

10.1371/journal.pone.0090346

10.1046/j.1365‐313X.2003.01810.x

10.1534/genetics.114.170746

Griffiths S. Wingen L. Pietragalla J. Garcia G. Hasan A. Miralles D. Calderini D.F. Ankleshwaria J.B. Waite M.L. Simmonds J. Snape J. Reynolds M..2015.Genetic dissection of grain size and grain number trade‐offs in CIMMYT wheat germplasm.PLoS ONE.doi:10.1371/journal.pone.0118847

10.1534/genetics.167.1.471

10.1007/s00122‐015‐2549‐2

10.2135/cropsci1972.0011183X001200020005x

10.1093/jxb/erl225

10.5897/JPBCS2015.0497

10.1007/s00122‐002‐1012‐3

House L.R., 1985, A guide to sorghum breeding

10.1038/ng.695

10.1007/s001220100541

10.1186/1746‐4811‐9‐29

10.1016/S0963‐9969(01)00167‐3

10.1093/genetics/141.1.391

10.1093/bioinformatics/bts444

10.2135/cropsci1985.0011183X002500020010x

10.1038/ncomms3320

10.1093/pcp/pcu187

10.2135/cropsci2007.09.0529

10.1126/science.1080585

10.1073/pnas.1215985110

10.1534/g3.113.008417

10.1371/journal.pgen.1004969

Murray S.C., 2012, Genomics of the Saccharinae, 479

10.2135/cropsci2008.01.0016

10.1007/s11032‐010‐9411‐7

10.1371/journal.pone.0057868

10.1038/nature07723

10.1126/science.269.5231.1714

Peterson B.G., 2014, PerformanceAnalytics: Econometric tools for performance and risk analysis, R package version, 1, 3541

10.1111/j.1365-294X.2004.02396.x

R Core Development Team, 2013, R: A language and environment for statistical computing

10.1073/pnas.201394398

Reynolds M., 2015, Proc. of the Int. TRIGO (Wheat) Yield Potential Workshop

10.1021/jf503651t

10.1007/978-94-017-3624-4_5

10.1007/s11032‐008‐9182‐6

10.1016/j.fcr.2006.07.004

10.1093/jxb/eru061

10.1086/502802

10.1104/pp.114.235424

10.1016/j.fcr.2010.11.013

10.1270/jsbbs.59.217

10.3389/fgene.2013.00093

10.1007/s00122‐010‐1312‐y

10.1093/pcp/pcs147

10.1007/s00122‐009‐0993‐6

10.1007/s001220051538

10.1007/s00122‐014‐2435‐3

10.2135/cropsci2015.03.0139

10.3835/plantgenome2012.07.0016

10.1111/tpj.12394

10.1038/90135

10.1038/nbt.1621

10.1016/j.fcr.2006.07.010

USDA–ARS–National Genetic Resources Program, 2014, Germplasm Resources Information Network (GRIN)

10.1016/j.fcr.2008.06.001

10.3168/jds.2007‐0980

10.1023/A:1026501430422

10.1016/S1672‐6308(13)60179‐1

10.1093/jxb/erp019

10.1104/pp.112.206870

10.1534/genetics.115.177170

10.1371/journal.pgen.1003264

Thông tin
Thông tin xuất bản

Plant Genome

Tập 9 Số 2

Thông tin tác giả