Identification of QTLs associated with seed protein concentration in two diverse recombinant inbred line populations of pea

Krishna Kishore Gali; Ambuj Jha; Bunyamain Tar'an; Judith Burstin; Gregoire Aubert; Dengjin Bing; Gene Arganosa; Thomas D Warkentin

doi:10.3389/fpls.2024.1359117

Identification of QTLs associated with seed protein concentration in two diverse recombinant inbred line populations of pea

Front Plant Sci. 2024 Mar 11:15:1359117. doi: 10.3389/fpls.2024.1359117. eCollection 2024.

Authors

Krishna Kishore Gali¹, Ambuj Jha^{1

2}, Bunyamain Tar'an¹, Judith Burstin³, Gregoire Aubert³, Dengjin Bing⁴, Gene Arganosa¹, Thomas D Warkentin¹

Affiliations

¹ Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada.
² School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.
³ Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France.
⁴ Agriculture and Agri-Food Canada, Lacombe, AB, Canada.

Abstract

Improving the seed protein concentration (SPC) of pea (Pisum sativum L.) has turned into an important breeding objective because of the consumer demand for plant-based protein and demand from protein fractionation industries. To support the marker-assisted selection (MAS) of SPC towards accelerated breeding of improved cultivars, we have explored two diverse recombinant inbred line (RIL) populations to identify the quantitative trait loci (QTLs) associated with SPC. The two RIL populations, MP 1918 × P0540-91 (PR-30) and Ballet × Cameor (PR-31), were derived from crosses between moderate SPC × high SPC accessions. A total of 166 and 159 RILs of PR-30 and PR-31, respectively, were genotyped using an Axiom® 90K SNP array and 13.2K SNP arrays, respectively. The RILs were phenotyped in replicated trials in two and three locations of Saskatchewan, Canada in 2020 and 2021, respectively, for agronomic assessment and SPC. Using composite interval mapping, we identified three QTLs associated with SPC in PR-30 and five QTLs in PR-31, with the LOD value ranging from 3.0 to 11.0. A majority of these QTLs were unique to these populations compared to the previously known QTLs for SPC. The QTL SPC-Ps-5.1 overlapped with the earlier reported SPC associated QTL PC-QTL-3. Three QTLs, SPC-Ps-4.2, SPC-Ps-5.1, and SPC-Ps-7.2 with LOD scores of 7.2, 7.9, and 11.3, and which explained 14.5%, 11.6%, and 11.3% of the phenotypic variance, respectively, can be used for marker-assisted breeding to increase SPC in peas. Eight QTLs associated with the grain yield were identified with LOD scores ranging from 3.1 to 8.2. Two sets of QTLs, SPC-Ps-2.1 and GY-Ps-2.1, and SPC-Ps-5.1 and GY-Ps-5.3, shared the QTL/peak regions. Each set of QTLs contributed to either SPC or grain yield depending on which parent the QTL region is derived from, thus confirming that breeding for SPC should take into consideration the effects on grain yield.

Keywords: Pisum sativum; QTL; SNP genotyping; marker-assisted selection; vegetable protein.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by the Saskatchewan Ministry of Agriculture’s Strategic Research Initiative (SRI) under the research project Pea Protein ‘Omics Determination (P-POD; project # 20180436).