Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer

Patricia Cabas-Lühmann; Andrés R Schwember; Osvin Arriagada; Ilaria Marcotuli; Iván Matus; Christian Alfaro; Agata Gadaleta

doi:10.3389/fpls.2024.1305196

Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer

Front Plant Sci. 2024 Mar 14:15:1305196. doi: 10.3389/fpls.2024.1305196. eCollection 2024.

Authors

Patricia Cabas-Lühmann¹, Andrés R Schwember¹, Osvin Arriagada², Ilaria Marcotuli³, Iván Matus⁴, Christian Alfaro⁵, Agata Gadaleta³

Affiliations

¹ Departamento de Ciencias Vegetales, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago, Chile.
² Centro de Estudios en Alimentos Procesados (CEAP), Talca, Chile.
³ Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy.
⁴ Instituto de Investigaciones Agropecuarias (INIA), Centro Regional Quilamapu, Chillán, Chile.
⁵ Instituto de Investigaciones Agropecuarias (INIA), Centro Regional Rayantue, Rancagua, Chile.

Abstract

Wild emmer (Triticum turgidum ssp. dicoccoides) genotypes were studied for their high-nutritional value and good tolerance to various types of stress; for this reason, several QTL (quantitative trait loci) studies have been conducted to find favorable alleles to be introgressed into modern wheat cultivars. Given the complexity of the QTL nature, their interaction with the environment, and other QTLs, a small number of genotypes have been used in wheat breeding programs. Meta-QTL (MQTL) analysis helps to simplify the existing QTL information, identifying stable genomic regions and possible candidate genes for further allele introgression. The study aimed to identify stable QTL regions across different environmental conditions and genetic backgrounds using the QTL information of the past 14 years for different traits in wild emmer based upon 17 independent studies. A total of 41 traits were classified as quality traits (16), mineral composition traits (11), abiotic-related traits (13), and disease-related traits (1). The analysis revealed 852 QTLs distributed across all 14 chromosomes of wild emmer, with an average of 61 QTLs per chromosome. Quality traits had the highest number of QTLs (35%), followed by mineral content (33%), abiotic-related traits (28%), and disease-related traits (4%). Grain protein content (GPC) and thousand kernel weight (TKW) were associated with most of the QTLs detected. A total of 43 MQTLs were identified, simplifying the information, and reducing the average confidence interval (CI) from 22.6 to 4.78 cM. These MQTLs were associated with multiple traits across different categories. Nine candidate genes were identified for several stable MQTLs, potentially contributing to traits such as quality, mineral content, and abiotic stress resistance. These genes play essential roles in various plant processes, such as carbohydrate metabolism, nitrogen assimilation, cell wall biogenesis, and cell wall extensibility. Overall, this study underscores the importance of considering MQTL analysis in wheat breeding programs, as it identifies stable genomic regions associated with multiple traits, offering potential solutions for improving wheat varieties under diverse environmental conditions.

Keywords: QTL; abiotic-related traits; disease-related traits; meta-QTL analysis; mineral composition; quality traits; wild emmer.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This article was funded by the Agencia Nacional de Investigación y Desasrrollo de Chile (ANID) grant number 1210092, Fondecyt Regular (AS, IvM, and CA).