A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat

Abstract

A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number. Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between '20828' and 'Chuannong16' was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23-45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of 'Chinese Spring' and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work.

Several stably expressed QTL for spike density of common wheat (Triticum aestivum) in multiple environments

“…The average values were used for the subsequent analysis. Among these traits, data of PH, SL, ET, SNS and TKW (in 2017CZ, 2017WJ, 2018WJ and 2018YA) and that of KL and KW (in 2017CZ, 2017YA, and 2018YA) were reported in our previous studies (Liu et al, ; Ma, Zhang, et al, ).…”

“…These excellent agronomic traits make 20828 be widely utilized as a breeding parent for the past 10 years. CN16 is a 1BL/1RS translocation carrier (Qi et al, ) with strong tillering ability (Liu et al, ).…”

“…The genetic linkage map utilized in this study was previously constructed by Wheat55K SNP array (Liu et al, ), and 10 SSR markers were added to the map on chromosome 1B (Ma, Ding, et al, ). A total of 12,109 SNP marker loci were distributed evenly on 21 chromosomes, with an average of 2,600 markers per chromosome, and the average distance between markers was about 0.1 cM (Ma, Ding, et al, ).…”

“…CN16 carries the 1BL/1RS translocation (Qi et al, ), and thus, the 1RS‐ or 1BS‐specific markers showed co‐segregation and distorted segregation in the 2CN RIL population (Liu et al, ). Therefore, the constructed genetic map did not cover 1BS but 1BL only (Ma, Ding, et al, ).…”

“…Therefore, the constructed genetic map did not cover 1BS but 1BL only (Ma, Ding, et al, ). Among the RILs, the lines containing 1BS ( n = 34) and 1RS ( n = 139) had been identified (Liu et al, ). Here, we calculated SD difference between the two groups based on the eight environments and BLUP value using Student's t test by SPSS ( p < .05).…”