QTL Manning And Genetic Basis Of Heterosis For Yield And Fiber Aualitv Traits In Upland Cotton(G.hirsutum L.)

Cotton(Gossypium sp.)is the most cultivated renewable natural fiber source worldwide.Genetic improvement of cotton yield and fiber quality is the primary goal of cotton breeding.Yield and fiber quality traits are quantitative in nature and possess complex genetic mechanisms.Furthermore,significant heterosis exists in yield and fiber quality traits of cotton.In this study,based on an upland cotton recombinant inbred lines(RILs)population derived from the hybrid of HS46 × MARCABUCAG8US-1-88,a high density map was constructed by a cotton 63K single nucleotide polymorphism(SNP)assay.To elucidate the genetic basis of upland cotton heterosis,we further developed an "immortalized F2"(IF2)and two reciprocal backcross(BCF1)populations based on RIL and their parents.The QTL mapping and the analysis of genetic effects for yield and fiber quality traits were explored using composite interval mapping and inclusive composite mapping methods in these four populations.The main results were as follows:(1)Construction of the high density SNP genetic map in upland cottonBased on an upland cotton RIL population,a 1784.28 cM(centimorgans)linkage map,harboring 2618 polymorphic SNP markers,was constructed by the cotton 63K SNP assay,which had 0.68 cM per marker density.The arrange of most SNP loci in the genetic map was consistent with that in the physical map of upland cotton,indicating that the genetic map have good collinearity with the physical map.Among the mapped SNP loci,13.29%showed segregation distortion.Furthermore,most segregation distortion loci occurred in the clusters on the same chromosome or within the same segregation distorted region(SDR)and skewed to the same allele.(2)Construction of genetic population for heterosis in upland cottonA set of IF2 population including 376 crosses was created by incomplete diallel crossing based on the upland cotton RIL population.In addition,two BCF1 populations,named as HSBCF1 and MARBCF1,derived from HS46 and MARCABUCAG8US-1-88 backcrossed with 188 RIL lines,respectively,were constructed.Both IF2 and BCF-populations were heterozygous.The yield and fiber quality traits in IF2 and BCF1 populations have characters of quantitative traits,and means of most traits in some crosses of IF2 and BCFi populations were beyond those of the parents(HS46 and MARCABUCAG8US-1-88).IF2 and BCF1 populations thus were suitable resources for heterosis genetic studies and breeding.In addition,IF2MPH,HSBCF1MPH,and MARBCF1MPH datasets were obtained by calculating the mid-parent heterosis values(MPH)of each hybrid line in IF2,HSBCFi,and MARBCFi populations.These datasets provide an opportunity for analyzing heterosis by mapping heterotic QTLs,rather than single analyses of direct trait performance.(3)Genetic characteristics of yield and fiber quality traits of upland cottonIn RIL,IF2,HSBCF1 and MARBBCFi populations,the broad-sense heritability of lint percentage(LP)and fiber length(FL)was higher,while the heritability of fruit branches per plant(FB)and fiber uniformity(FU)was lower.Other traits showed moderate heritability,indicating that yield and fiber quality traits were controlled by both genetic and environmental effects.In correlation analysis,lint yield(LY)was significantly and positively correlated with seed cotton yield(SY),boll numbers per plant(BN)and boll weight(BW)in all populations,therefore,yield could be increased by improving BN and BW.Further SY and LY showed significant and positive correlation to micronaire(MIC)value in all populations,while significant and negative correlation to fiber elongation(FE)and fiber strength(FS)and significant and positive correlation to FU in three populations.Therefore,by optimizing MIC,improving FU,and moderately reducing FS,the goal of cultivating upland cotton varieties with high yield and good quality can be achieved.(4)Heterosis performance of yield and fiber quality of upland cottonIn RIL population,significant inbreeding depression was observed for FB,BN,SY,and LY;small inbreeding depression was observed for MIC and FE.In IF2 and two BCF1 populations,high levels of heterosis for SY,LY,and BW were observed;a relatively high level of heterosis for MIC,FL and FS was observed.(5)The QTL mapping and genetic effects for heterosis of yield and fiber quality traits in upland cottonAt the single-locus level,a total of 205 yield traits QTLs and 196 fiber quality traits QTLs were detected in the RIL,IF2 and two BCF1 datasets,and 138 yield traits heterotic QTLs and 65 fiber quality traits heterotic QTLs were detected in the IF2MPH and two BCF1MPH datasets using the composite interval mapping(CIM)approach.Analysis of genetic effects of QTLs detected in different datasets showed that the genetic basis of heterosis of yield and fiber quality were varied in different populations.Partial dominance and overdominance were the main cause of heterosis in the IF2 population,while additive effect and over-dominance were the main genetic bases of heterosis in two BCF1 populations.In addition,the various genetic components to yield heterosis presented trait specificity.Overdominance and additive effect were the main cause of heterosis of SY,LY,BW,and LP.Overdominance,partial dominance,and additive effect all had roles of the heterosis for BN.Overdominance was the most important contributor to the heterosis of FB.While the contribution rates of each genetic component to the heterosis of fiber quality traits were similar,which were mainly additive effect and overdominance.At the two-locus level,a total of 160 yield traits main-QTLs(m-QTLs)and 130 fiber quality traits m-QTLs,and 395 yield traits epistasis-QTLs(e-QTLs)and 283 fiber quality traits e-QTLs,were detected in the RIL,IF2 and two BCF1 datasets;86 yield traits heterotic m-QTLs and 25 fiber quality traits heterotic m-QTLs,and 254 yield traits heterotic e-QTLs and 137 fiber quality traits heterotic e-QTLs,were detected in the IF2MPH and two BCF1MPH datasets by inclusive composite interval mapping(ICIM)approach.Phenotypic variances(PV)explained by e-QTLs were higher than those by m-QTLs in most of the traits,indicating that epistasis was important for the heterosis formation of yield and fiber quality.The epistasis occurred more frequently between complementary loci with no detectable main effects.Furthermore,the environment was a critical factor in the expression of these m-QTLs and e-QTLs.(6)The genetic characteristics of heterotic QTL of yield and fiber quality traits of upland cottonHeterotic QTLs detected in this study were not independent,and a subset overlapped with QTLs controlling trait performance.Both of them contributed to the performance of trait heterosis.The heterotic QTLs were not randomly distributed on chromosomes,but exists in clusters and hotspots.The clusters and hotspots should be used as a key region in the process of traits improved,which is benefit to accelerating the pace of the improvement of traits.Heterotic QTLs are sensitive to the environment,which should be taken into account in hybrid breeding of upland cotton.Altogether,additive effects,partial dominance,overdominance,epistasis and environmental interactions all contributed to the heterosis of yield and fiber quality traits in upland cotton,with overdominance and epistasis more important than the others.Furthermore,the heterosis genes can be further exploited because of the detection of significant heterotic QTLs,which will greatly accelerate the hybrid breeding process of upland cotton.