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

Akerke Amalova; Kanat Yermekbayev; Simon Griffiths; Saule Abugalieva; Adylkhan Babkenov; Elena Fedorenko; Aigul Abugalieva; Yerlan Turuspekov

doi:10.7717/peerj.14324

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

PeerJ. 2022 Nov 9:10:e14324. doi: 10.7717/peerj.14324. eCollection 2022.

Authors

Akerke Amalova^{1

2}, Kanat Yermekbayev^{1

3}, Simon Griffiths³, Saule Abugalieva^{1

2}, Adylkhan Babkenov⁴, Elena Fedorenko⁵, Aigul Abugalieva⁶, Yerlan Turuspekov^{1

2}

Affiliations

¹ Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.
² Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
³ The John Innes Centre, Norwich, United Kingdom.
⁴ A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan.
⁵ North Kazakhstan Agricultural Experimental Station, Petropavlovsk, Kazakhstan.
⁶ Kazakh Research Institute of Agriculture and Plant Industry, Almalybak, 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.

Keywords: Mapping population; Quantitative trait loci; Recombinant inbred lines; Triticum aestivum L.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bread
Genome-Wide Association Study
Kazakhstan
Plant Breeding
Polymorphism, Single Nucleotide / genetics
Quantitative Trait Loci* / genetics
Triticum* / genetics

Grants and funding

This research was funded by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (Grant No. AP08855387). The publication cost was covered by ZALMA Ltd (Almaty, Kazakhstan). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.