QTL Mapping And Candidate Gene Prediction Of Seedling And Grain Size Traits In Barley

Since domesticated about 10,000 years ago in the Fertile Crescent,barley?Hordeum vulgare L.?has become one of the most important cereal crops cultivated around the world,and is widely used as animal feed,food,potential healthy food products and is a major raw material for malting and brewing industries.With the rapid growth of the global population,the continuous reduction of arable land worldwide and the continuous improvement of people's quality of life,improving barley yield and quality are still important targets of current barley genetic research and breeding programs.Seedling traits play an important role in barley yield and quality formation.Grain size is a crucial component of barley yield and quality.Despite this,little is known about the genetic and molecular mechanisms of seedling and grain size traits in barley.Untangling the genetic factors controlling seedling and grain size traits is of great significance for the genetic improvement of barley with high-yield and top-quality.In this study,an integrated high-density genetic linkage map containing 1894 SNP markers and 68 SSR markers was constructed based on 122 lines of barley DH population?“Huaai 11”דHuadamai 6”?.We mapped QTL for 21 seedling characteristics under hydroponic culture,and 9 grain size traits assessed for three consecutive years in a DH population.The main results are as follows:1. QTL mapping of seedling characteristics in barleyTo explore the genetic regulation of barley seedling traits,we evaluated the 21seedling traits of barley DH population under hydroponic culture.Based on the constructed high-density genetic map,the QTL analysis of 21 seedling traits under hydroponic conditions was carried out by using the complete interval mapping method?ICIM?.A total of 70 QTLs were identified in 17 of the 21 seedling characteristics using ICIM mapping.No QTL was identified for second leaf length?SELL?,first leaf width?FILW?,third leaf width?THLW?and fourth leaf width?FOLW?.These 70 QTLs were distributed over all chromosomes except 4H,and,individually,accounted for5.01%-77.78%of phenotypic variation.Ten pleiotropic or tightly linked QTLs that affected at least two seedling traits were identified on the 2H,3H and 7H chromosomes.Among them,a significant region located at 651.53-652.51 Mb?near Vrs1 locus?on chromosome 2H with pleiotropic or tightly linkage effects on main root number?MRN?,seedling fresh weight?SFW?,stem-and-leaves fresh weight?SLFW?,stem-and-leaves dry weight?SLDW?,first leaf area?FILA?,second leaf area?SELA?,fourth leaf area?FOLA?and second leaf width?SELW?,can explained 12.05%-30.50%phenotypic variation.We hypothesized that QTLs for seedling traits in this region may be a result of the pleiotropic effect of the Vrs1 locus.2. Dynamic expression of QTLs in barley seedling characteristicsTo explore the dynamic inheritance of seedling traits at different developmental stages,we performed dynamic QTL analysis for five seedling traits including leaf age?LAG?,seedling height?SH?,seedling fresh weight?SFW?,maximum root length?MRL?and number of main roots?MRN?at four growth stages(13^th,20^th,27^thand 34^thdays after germination).A total of 42 QTLs were detected on all chromosomes except for 4H and6H chromosomes.Phenotypic variation explained by single QTL ranged from 6.03%to73.86%for LAG,from 5.49%to 24.90%for SH,from 7.85%to 32.39%for SFW,from8.08%to 16.23%for MRL and from 7.71%to 31.28%for MRN.The dynamic expression analysis with developmental changes for 42 QTLs that identified in four growth stages showed that the QTLs of these five seedling traits showed selectively expressed with growth stages,that is,some QTLs only affect the corresponding traits at a certain stage,and some QTLs persistently affected the corresponding traits at multiple growth stages.We identified 9 regions on the 2H,3H and 7H chromosomes that were expressed at least in two developmental stages,including 2,2,1,and 4 sites for SH,SFW,LAG,and MRL.These 9 regions showed different developmental effects at different growth stages.3. QTL mapping of grain size traits in barleyTo reveal the genetic basis of barley grain size traits,we evaluated 9 traits determining grain size,including thousand grain weight?Tgw?,grain length?Gl?,grain width?Gw?,grain length-width ratio?Lwr?,grain area?Ga?,grain perimeter?Gp?,grain diameter?Gd?,grain roundness?Gr?,and the factor form density?Ffd?,in a double haploid?DH?population for three consecutive years.Based on SNP-based high density genetic map,we performed QTL analysis of 9 grain size traits in a DH population using five mapping methods.A total of 60 reliable QTLs?QTLs of the same trait repeatedly detected in at least two years environment and in multiple mapping methods?for 9 grain size traits were identified on all 7 chromosomes,including 7,8,9,7,9,6,6,4,and 4reliable QTLs for Tgw,Gl,Gw,Lwr,Ga,Gp,Gd,Gr,and Ffd,respectively.The phenotypic variation explained by each reliable QTL ranged from 0.75 to 70.03%,with a LOD value ranging from 3.42 to 80.98.In addition,we also identified 27 QTL hotspots that regulate grain size traits,which are distributed on all chromosomes except the 6H.4. Comparative genomic analysis of grain size traits in barleyTo explore the genetic correspondence for grain size-related genes in diverse cereal species,we collected 148 different genes from cereal crops associated with grain size,including 94 rice genes,40 maize genes,and 14 wheat genes.Based on the comparative genomics approach,we identified 164 barley orthologs from 112 genes from other cereal species.Among these 164 barley orthologous genes,a total of 33 barley orthologs were identified as potential candidate genes that determine barley grain size,suggesting that some grain size-related genes in other cereals may have conserved functions in barley.Additionally,we also collected 38 barley genes to explore whether they also affect barley grain size and weight.Among these 38 barley genes,12 were identified as potential candidate genes affecting barley grain size and weight,suggesting that some barley yield-related genes were associated with grain size and weight.In summary,this research revealed the genetic characteristics of barley seedlings and grain size traits,and provides potential candidate genes.These results enhance the understanding of the genetic basis of barley seedlings and grain size traits,and provide some theoretical support for the breeding of new varieties with high-yield and top-quality in barley.