Abstract
BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90 K and 660 K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8 Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4–725.8 Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.
Highlights
Identification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS)
Marker coverage and genetic diversity After filtering, 326,570 polymorphic single nucleotide polymorphism (SNP) were employed for genome-wide association study (GWAS) analysis; 10,780 were from the wheat 90 K SNP array and 315,790 came from the wheat 660 K SNP array (Additional file 5: Table S4; Additional file 6: Figure S2a)
Among polymorphic SNP markers, 39.7, 49.4 and 10.9% were from the A, B and D genomes, respectively
Summary
Identification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Grain shape, spike architecture, plant height (PH), and flag leaf related traits can affect GY through effects on photosynthetic intensity, grain filling and dry matter translocation [5,6,7,8] These traits have higher heritabilities (h2) than GY and are easier to select in small plots at the early stages of breeding programs. Previous studies showed that increased yield potential in the YHRVWZ was largely associated with increased kernels per square meter, biomass and harvest index, and reduced PH [5, 6] Those improvements were mainly attributed to the use of dwarfing genes (Rht, Rht, Rht and Rht24) and the 1BL.1RS translocation lines [8,9,10,11,12,13]. It is believed that further improvement in yield potential can be achieved only by a detailed understanding of its genetic architecture combined with marker-assisted selection (MAS)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
