Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat

Abstract

Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main quantitative trait loci (QTLs) that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map QTLs for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as recombination-rich areas in all chromosomes except chromosome 1B. Both the genetic map and the physical map showed a significant correlation, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43 cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11 mm. A total of 43 QTLs were identified, including eight QTLs for plant height (PH), 11 QTLs for thousand grain weight (TGW), 15 QTLs for grain length (GL), and nine QTLs for grain width (GW), which explained 1.36–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci (Qph.nwafu-4B and Qph.nwafu-4D) that determined plant height. The explanation rates of phenotypic variation were 7.39–12.26% and 20.11–27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43–6.85% for phenotypic variation. Two co-segregating KASP markers were developed, and the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB, respectively. Qph.nwafu-4B, controlling plant height, and Qtgw.nwafu-4B, controlling TGW, had an obvious linkage relationship, with a distance of 7–8 cM. Breeding is based on molecular markers that control plant height and thousand-grain weight by selecting strains with low plant height and large grain weight. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43–6.85%. Three loci that affected grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2, and Qgl.nwafu-6B, illustrating the explanation rates of phenotypic variation as 6.72–9.59%, 5.62–7.75%, and 6.68–10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.

Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.)

“…Similarly, four MTAs were identified on 3D, 2D, 3A, and 2B for TKW. MTAs for TKW on the same chromosomes in different mapping populations were also identified in earlier reports on 1B [ 27 ], 2B [ 28 , 91 ], 2D [ 25 , 80 , 91 , 92 , 93 ], 3A [ 88 , 93 , 94 , 95 ] at different chromosomal locations. Cabral et al [ 27 ] identified a QTL, i.e., QGwt.crc-2B-2 , on the 2B chromosome, located at a confidence interval of 92.9–96.0 cM, which was similar to the MTA ( AX-95194336 ) detected in the current study on the same chromosome at 96.2 Mb.…”

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

“…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.…”

Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L.

“…Genetic map or genetic linkage map refers to the relative location and genetic distance of a gene or molecular marker on a chromosome, which is different from the real distance in a physical map ( Meng et al, 2015 ; Yagi et al, 2017 ; Lv et al, 2021 ). Genetic distance in a genetic map is calculated from the recombination rate of genes or markers.…”