The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice

ABSTRACT Low-coveragewhole-genomesequencingisaneffectivestrategyforgenome-wideassociationstudiesinhu-mans,duetotheavailabilityoflargereferencepanelsforgenotypeimputation.However,itisunclearwhetherthis strategy can be utilized in other species without reference panels. Using simulations, we show that thisapproachisevenmorerelevantininbredspeciessuchasrice(OryzasativaL.),whichareeffectivelyhaploid,allowingeasyhaplotypeconstructionandimputation-basedgenotypecalling,evenwithouttheavailabilityoflargereferencepanels.Wesequenced203ricevarietieswithwell-characterizedphenotypesfromtheUnitedStatesDepartmentofAgricultureRiceMini-CoreCollectionatanaveragedepthof1.53andusedthedataformapping three traits. For the first two traits, amylose content and seed length, our approach leads to directidentificationofthepreviouslyidentifiedcausalSNPsinthemajor-effectloci.Forthethirdtrait,pericarpcolor,an important trait underwent selection during domestication, we identified a new major-effect locus.AlthoughknownlocicanexplaincolorvariationinthevarietiesoftwomainsubspeciesofAsiandomesticatedrice,japonicaandindica,thenewlocusidentifiedisuniquetoanotherdomesticatedricesubgroup,aus,andtogether with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of aunique genetic basis of white pericarp in aus provides an example of convergent evolution during ricedomesticationand suggests thatausmayhaveadomesticationhistoryindependent ofjaponicaand indica.Key words: inbreeding, GWAS, rice, pericarp colorWang H., Xu X., Vieira F.G., Xiao Y., Li Z., Wang J., Nielsen R., and Chu C. (2016). The Power of Inbreeding:NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. Mol. Plant. 9, 975–985.

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