Construction Of High-density Genetic Map And QTL Analysis Of Yield And Agronomic Traits In Foxtail Millet

Foxtail millet [Setaria italica?L.?P.Beauv.],a crop of historical importance in China,is still a very important crop in arid and semiarid regions of northern China.Grains of foxtail millet are enriched for various amino acids and nutritive minerals and the crop possesses some advantageous traits,e.g.high photosynthetic efficiency and drought tolerance.Because of its small genome?⁵15 Mb?with a small number of chromosomes?2n=2x=18?and inbreeding nature,foxtail millet has been adopted as a model crop for studying C-4 photosynthesis,stress biology and biofuel traits.Therefore,development of high yielding,high quality,and stress resistant foxtail millet cultivars is an important goal for foxtail millet scientists.Virtually most of the important agronomic traits and all yield component traits of foxtail millet are quantitative inheritance,so it takes much time to increase yield and improve quality through traditional genetic improvement methods.Based on QTL identified for quantitative traits,molecular marker-assisted selection?MAS?can rapidly increase yield and improve quality of foxtail millet cultivars.The genome information for foxtail millet also provides an important resource for crop improvement.To date,a large number of foxtail millet SSR markers have been developed,but SSRs used to construct a genetic map are limited.Furthermore,the available foxtail millet genetic maps have a limited number of markers,and the QTL identified are far from the linked makers.Therefore,it is urgent to explore more SSR markers to construct high-density linkage maps and identify many more QTL for marker-assisted selection in foxtail millet.In the present study,two foxtail millet cultivars Yugu1 and Longgu7 were crossed to establish an F₂ population.SSR markers developed from the foxtail millet genome sequence were applied to construct genetic map and explore favorable QTL alleles from either parent to increase yield and optimize agronomic traits.The results will be valuable for future research on improvement of foxtail millet yield and agronomic traits.The main results are as follows: 1.Development of SSR markersA total of 10598 SSR markers were developed from the ‘Yugu1' reference genomic sequence.The number of SSR markers on the chromosomes ranged from 658 to 1874,approximately covering 99.89% of the physical length of the genome.The marker density along each chromosome ranged from 16.17 to 31.78 markers per Mb,with an average of 26.25 markers per Mb.Among nine chromosomes,the number of markers on chromosome 9 was the highest and the highest marker density was on chromosome 9?31.78/Mb?,and the number of markers on chromosome 8 was the lowest?16.17/Mb?.The most abundant type of SSR was pentanucleotides?4780,45.85%?,followed by hexanucleotides?2295,22.01%?,tetranucleotides?1925,18.47%?,trinucleotides?782,7.5%?,dinucleotides?376,3.6%?and mononucleotides?267,2.56%?.2.Genotyping of F₂ populationAmong 10598 SSR markers screened,1013?9.6%?showed clear polymorphism between Yugu1 and Longgu7.The polymorphic markers were used to genotype the?Yugu1×Longgu7?F₂ population,and 1035 loci were obtained.All these SSR markers in the genetic map covered 395.65 Mb of physical length,which spanned about 76.8% of the entire recombinational length of the foxtail millet genome??515 Mb?.Through Chi-square??²?,the results showed that a total of 220 SSR loci distorted from segregation ratio?P<0.05?,accounting for 21.3% of the total locus.3.Construction of genetic linkage mapThe 1035 loci were mapped into nine chromosomes,covering 1318.8 c M,with average distance of 1.27 cM between adjacent markers.Loci were not evenly distributed over chromosomes.For example,Chr.8 was mapped with 186 loci,whereas Chr.1 and Chr.4 were mapped with only 86 and 67 loci,respectively.In terms of recombinational length,the longest chromosome was Chr.9,which spanned 226.4 c M,and the shortest was Chr.7,which spanned only 102.9 c M.For the average distance between markers,Chr.9 was the largest?2.02 c M?,Chr.8 was the smallest?0.67 c M?.4.QTL analysis for yield and agronomic traits of foxtail milletA total of 29 QTL were identified for 11 agronomic and yield traits with a range of 1⁶ QTL per trait.The percentage of phenotypic variance explained by individual QTL for each trait ranged from 7.0% to 14.3%.Among these QTL,18 were detected from both combined analysis and single environment analysis and 2 were detected only from combined analysis.There were 22 favorable alleles originating from Yugu1 and 6 from Longgu7.For each QTL,the favorable allele originated from the same parent as indicated by the additive effect of QTL,except that q TGW5.1 were conferred by different parents in 2014 and combined.8 QTL?q LMS1.1,q DMS1.1,q NMS1.1,q MPL1.1,q MPD1.1,q SWP1.1,q PWP1.1 and q GWP1.1?controlling different traits were detected in the same interval of Chr.1.