A High-density Genetic Map And QTLs For Yield Traits In Wheat Based On RNA-Seq

Wheat(Triticum aestivum L.)is the most important cereal crop in the world.A high genetic map constructed of wheat(Triticum aestivum L.)were conducted using a population of 176 recombinant inbred lines(RILs)derived from “Shannong 0431 × Lumai 21” with QTL analysis for yield traits based on RNA-Seq.The main results are follows:First,Shannong 0431 was sequenced and got 65.15 Gb clean reads processed from 66.09 Gb raw reads.We got 85.74% alignment and obtained 234641 transcripts with average length 1599.5bp,N50 length 2229 bp,GC content 50.82%.For trinity,we got 3910 sequences.Lumai 21 was sequenced and got 64.26 Gb clean reads processed from 65.24 Gb raw reads.We got 86.20% alignment and obtained 228827 transcripts with average length 1590.89 bp,N50 length 2225 bp,GC content 50.91%.For trinity,we got 3965 sequences.Second,we screened 188524 markers with 172070 SNPs and 16454 INDELs.With these,132240 markers were annotated on Chinese Spring annotation,49201 on parents' annotation,7083 unannotated.We identified 45996 unigenes from 188524 markers and screened 18274 unigene with the numbers of genotype 0/0 and 1/1 larger than 20%.Third,a number of 3848 BINs were used to construct genetic maps.The final map spanned a total length of 11421.27 cM across 63 linkage groups with 3952.25 cM(34.6%),5177.14cM(45.3%)and 2291.88 cM(20.1%)in lengths;1369,1819 and 660 in BINs;23,22 and 18 in groups;2.89 cM,2.85 cM and 3.47 cM average distances for the A,B and D genomes,respectively.Forth,A total of 515 additive QTLs(1031 QTLs for trait-environment combinations)were detected except for 3DS in the eight environments and AV.230 QTLs showed positive additive effects with Shannong 0431 increasing the effects of QTLs,whereas 285 QTLs were negative effects with Lumai 21 increasing the QTL effects.75 relatively high-frequency(RHF)QTLs in more than four environments and/or in AV were located,including ten traits(PH,TGW,SL,BSSS,TSS,FSS,GL,GW,GLW and FFD)with the average contributions ranging from 4.40-27.83%.31 RHF-QTLs showed positive additive effects with Shannong 0431 increasing the effects of QTLs,whereas 44 QTLs were negative effects with Lumai 21 increasing the QTL effects.And we detected 34 stable RHF-QTLs with over 10% contributions.