Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

Akerke Amalova; Saule Abugalieva; Adylkhan Babkenov; Sandukash Babkenova; Yerlan Turuspekov

doi:10.7717/peerj.11857

Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

PeerJ. 2021 Jul 27:9:e11857. doi: 10.7717/peerj.11857. eCollection 2021.

Authors

Akerke Amalova^{1

2}, Saule Abugalieva^{1

2}, Adylkhan Babkenov³, Sandukash Babkenova³, Yerlan Turuspekov^{2

4}

Affiliations

¹ Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
² Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.
³ A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Akmola Region, Kazakhstan.
⁴ Faculty of Agrobiology, Kazakh National Agrarian University, Almaty, Kazakhstan.

Abstract

Background: Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach.

Methods: A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m² (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits.

Results: Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.

Keywords: Common wheat; Drought tolerance; GWAS; Marker-trait associations; Quantitative trait loci.

Grants and funding

This study was supported by (1) the grant AP08855387 “Nested association mapping for gene discovery and deployment for improvement of yield, quality, and disease resistance in bread wheat” for 2020–2022 by the Ministry of Education and Science of the Republic of Kazakhstan, and (2) BR10765056 “Creation of highly productive varieties and hybrids of grain crops based on the achievements of biotechnology, genetics, physiology, plant biochemistry for their sustainable production in various soil and climatic zones of Kazakhstan” within the framework of program-targeted financing by the Ministry of Agriculture of the Republic of Kazakhstan for 2021–2023. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.