Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva × Paragon mapping population harvested in three regions of Kazakhstan

Abstract

Background Although genome-wide association studies (GWAS) are an increasingly informative tool in the mining of new quantitative trait loci (QTLs), a classical biparental mapping approach is still a powerful, widely used method to search the unique genetic factors associated with important agronomic traits in bread wheat. Methods In this study, a newly constructed mapping population of Pamyati Azieva (Russian Federation) × Paragon (UK), consisting of 94 recombinant inbred lines (RILs), was tested in three different regions of Kazakhstan with the purpose of QTL identification for key agronomic traits. The RILs were tested in 11 environments of two northern breeding stations (Petropavlovsk, North Kazakhstan region, and Shortandy, Aqmola region) and one southeastern station (Almalybak, Almaty region). The following eight agronomic traits were studied: heading days, seed maturation days, plant height, spike length, number of productive spikes, number of kernels per spike, thousand kernel weight, and yield per square meter. The 94 RILs of the PAxP cross were genotyped using Illumina’s iSelect 20K single nucleotide polymorphism (SNP) array and resulted in the identification of 4595 polymorphic SNP markers. Results The application of the QTL Cartographer statistical package allowed the identification of 53 stable QTLs for the studied traits. A survey of published studies related to common wheat QTL identification suggested that 28 of those 53 QTLs were presumably novel genetic factors. The SNP markers for the identified QTLs of the analyzed agronomic traits of common wheat can be efficiently applied in ongoing breeding activities in the wheat breeding community using a marker-assisted selection approach.

Association Mapping of Quantitative Trait Loci for Agronomic Traits in a Winter Wheat Collection Grown in Kazakhstan

“…Four associations matched the results from studies of the UK reference mapping population Avalon × Cadenza, where QTL associations with HD, PH, and YM2 were identified in the northern, central, and southern regions of Kazakhstan [55]. Another four associations were identical to the genetic positions of QTLs identified in analyses of eight traits using 94 recombinant inbred lines of the mapping population of Pamyati Azieva × Paragon, which were tested in the northern and southern regions of Kazakhstan [56]. Three QTLs (QHD.ta.w.ipbb-2A.2, QHD.ta.w.ipbb-5B.1, and QSMD.ta.w.ipbb-3B) had identical genetic positions to QTLs identified in the GWAS of yield components in a spring wheat collection harvested under two water regimes in northern Kazakhstan [18] (Table S6).…”

“…Notably, the largest number of associations was identified for HD, PH, and NKS, which shows a wide range of variation of these traits in the two regions. The literature survey suggested that 23 of the 173 QTLs identified in our study had also been detected in previous QTL mapping studies and GWAS for HD, SMD, PH, SL, NKS, and YM2 [18,28,[50][51][52][53][54][55][56][57] (Table S6). The majority of these matches were found for PH (nine QTLs), followed by HD (six QTLs) and NKS (four QTLs) (Table S6).…”