High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map

Abstract

Background Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments. Results A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. Conclusions Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

“…For TW, six QTLs were identified on the 1A, 1B, 6A, and 7D chromosomes. Some QTLs were also identified in previous reports on the 1A [ 30 , 57 ], 6A [ 55 , 58 ], and 7D [ 29 , 30 , 46 ] chromosomes, at different positions.…”

“…The highest number of 12 QTLs were identified for PH on the 1B, 2B, 3A, 3B, 3D, 4A, 5A, 5D, 7B, and 7D chromosomes. Plant height is one of the important yield component traits in wheat, and therefore many QTLs were also identified in previous reports on chromosomes 1B [ 10 , 19 , 37 , 40 , 51 ], 2B [ 10 , 40 , 45 , 51 , 53 ], 3A [ 26 , 54 ], 3B [ 10 , 19 , 22 , 40 ], 4A [ 26 , 45 , 52 , 53 ], 5A [ 19 , 26 , 45 , 51 , 53 , 55 , 56 ], and 7B [ 10 ], at different positions. In addition, Alemu et al [ 52 ] identified a QTL on the 4A chromosome at 41cM, which was similar to that of QPH-4A and mapped at 41cM, explaining a 4.58% phenotypic variation.…”

“…Eight QTLs were identified for TKW on the 3A, 4A, 5A, 5B, 6A, and 7D chromosomes. Previous reports also identified some QTLs on the same chromosomes: 3A [ 10 , 19 , 24 , 50 , 56 ], 4A [ 19 , 31 , 46 , 50 ], 5A [ 23 , 29 , 40 , 57 ], 5B [ 20 , 29 , 40 , 45 , 52 , 53 , 54 , 57 ], 6A [ 23 , 29 , 31 , 37 , 46 , 48 , 50 , 52 , 53 , 55 , 56 , 57 ], and 7D [ 29 , 31 , 40 , 50 ], at different positions. In addition, three previous reports, i.e., Gahlaut et al [ 19 ], Edae et al [ 46 ], and Ramya et al [ 27 ] identified a QTL at 73 cM, 72.4 cM, and 70 cM, respectively, on the 5B chromosome, which was similar to the QTL ( QTKW-5B ) identified in the present study at 70.5–73.5 cM, on the same chromosome.…”

Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)

“…genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping are widely used methods to dissect the genetic basis of complex quantitative traits in crop plants. In the past decade, extensive efforts have been made to identify QTLs associated with grain yield and its component traits (Gao et al, 2015;Zhang et al, 2016;Jin et al, 2020;Isham et al, 2021;Kang et al, 2021;Li et al, 2022) in wheat through bi-parental populations based QTL mapping. Conventional QTL mapping mainly depends on structured populations like recombinant inbred lines (RIL), back-crosses (BC), and doubled haploids (DH).…”

Genome-wide association mapping in elite winter wheat breeding for yield improvement

“…Two main approaches to dissect the genetic basis of complex quantitative traits in crop plants are genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Many QTLs associated with yield-related traits in bread wheat have been identified in biparental populations (Gao et al 2015;Yu et al 2017;Milner et al, 2016;Zhang et al 2016;Jin et al 2020;Isham et al 2021;Kang et al 2021;Li et al 2022). At present, GWAS has become more frequently used as it allows to identify of parts of the complex, essential traits valid in a studied panel of genotypes (Breseghello and Sorrells 2006;Neumann et al 2011;Dodig et al 2012;Jiang et al 2015;Liu et al 2015;Hu et al 2015;Sukumaran et al 2015;Sukumaran et al 2018;Tadesse et al 2015;Lozada et al 2017;Sun et al 2017;Würschum et al 2017b;Bhatta et al 2018;Sheoran et al 2019;Sun et al 2017;Liu et al 2018;Akram et al 2021;Qaseem et al 2019;Garcia et al 2019).…”