QTL mapping and KASP marker development for seed vigor related traits in common wheat

Abstract

Seed vigor is an important parameter of seed quality, and identification of seed vigor related genes can provide an important basis for highly efficient molecular breeding in wheat. In the present study, a doubled haploid (DH) population with 174 lines derived from a cross between Yangmai16 and Zhongmai 895 was used to evaluate 10 seed vigor related traits in Luoyang during the 2018-2019 cropping season and in Mengjin and Luoning Counties during 2019-2020 cropping season for three environments. Quantitative trait locus (QTL) mapping of 10 seed vigor related traits in the DH population resulted in the discovery/identification of 28 QTLs on chromosomes 2B, 3D, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A and 7D, explaining 3.6-23.7% of the phenotypic variances. Among them, one QTL cluster for shoot length, root length and vigor index was mapped between AX-89421921 and Rht-D1_SNP on chromosome 4D in the physical intervals of 18.78-19.29 Mb (0.51 Mb), explaining 9.2-20.5% of the phenotypic variances. Another QTL for these traits was identified at the physical position 185.74 Mb on chromosome 5B, which was flanked by AX-111465230 and AX-109519938 and accounted for 8.0-13.3% of the phenotypic variances. Two QTLs for shoot length, shoot fresh weight and shoot dry weight were identified in the marker intervals of AX-109384026-AX-111120402 and AX-111651800-AX-94443918 on chromosomes 6A and 6B, explaining 8.2-11.7% and 3.6-10.3% of the phenotypic variance, respectively; both alleles for increasing phenotypic values were derived from Yangmai 16. We also developed the KASP markers for the QTL cluster QVI.haust-4D.1/QSL.haust-4D/QRL.haust-4D, and validated in an international panel of 135 wheat accessions. The germplasm, genes and KASP markers were developed for breeders to improve wheat varieties with seed vigor related traits.

Keywords: KASP marker; QTL cluster; QTLs; Triticum aestivum; seed vigor.

Figure 1

The growth of DH lines using the paper roll method.Three seeds are shown in each group, YM 16: Yangmai 16, ZM895: Zhongmai 895, Family I represent the lines of low seed vigor, Family II represent the lines of high seed vigor, Day1-Day 8 refer to days after germination.

Figure 2

Frequency distribution for seed vigor related traits in DH population in three environments and mean values. Green, red, blue and purple represent 2018XN, 2019MJ, 2019LN and mean value, respectively. 2018XN, 2019MJ, 2019LN and mean represent data from the Farm of Henan University of Science and Technology in 2018-2019, Mengjin County in 2019-2020, Luoning County in 2019-2020, and mean values of three environments, respectively. SL, Shoot Length; RL, Root Length; FSW, Fresh Shoot Weight; FRW, Fresh Root Weight; DSW, Dry Shoot Weight; DRW, Dry Root Weight; GR, Germination Rate; GE, Germination Energy; GI, Germination Index; VI, Vigor Index.

Figure 3

QTL mapping for seed vigor related traits in the Yangmai 16/Zhongmai 895 DH population. Markers’ names are shown on the right of vertical axis, and their genetic positions are shown in cM on the left. Green, red, blue and purple represent QTL mapped using data of 2018XN, 2019MJ, 2019LN and mean values, respectively.

Figure 4

QTL clusters in the Yangmai 16/Zhongmai 895 DH population.

Figure 5

Genotype calling screenshots of the KASP marker. Orange indicates the C allele of Yangmai 16, blue indicates the A allele of Zhongmai 895, and black indicates the blank control. The same below.

Figure 6

Allelic effects identified by the KASP marker in the natural population. Blue indicates the A allele of Zhongmai 895, and orange indicates the C allele of Yangmai 16. * and **, significant at P<0.05 and P<0.01, respectively.

Figure 7

QTLs of the DH population on chromosome 4D.