Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using GWAS

Authors: HANIF, UZMA - National University Of Sciences And Technology; ALIPOUR, HADI - Urmia University; GUL, ALVINA - National University Of Sciences And Technology; LI, JIN - Chinese Academy Of Agricultural Sciences; BIHAMTA, REZA - University Of Tehran; MOHAMMADI, VALIOLLAH - University Of Tehran; PEYGHAMBARI, SEYED ALI - University Of Tehran; AMIR, RABIA - National University Of Sciences And Technology; MUNIR, FAIZA - National University Of Sciences And Technology; LLYAS, MUHAMMAD KASHIF - National Agricultural Research Center - Pakistan; St Amand, Paul; Bernardo, Amy; Bai, Guihua

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2021
Publication Date: 7/18/2021
Citation: Hanif, U., Alipour, H., Gul, A., Li, J., Bihamta, R., Mohammadi, V., Peyghambari, S., Amir, R., Munir, F., Llyas, M., St. Amand, P.C., Bernardo, A.E., Bai, G. 2021. Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using GWAS. The Plant Genome. https://doi.org/10.1002/tpg2.20096.
DOI: https://doi.org/10.1002/tpg2.20096

Interpretive Summary: To study wheat genomic regions associated with local wheat adaptation, 512 wheat landraces from the Fertile Crescent in Iran and Pakistan were genotyped with high-density, genome-wide DNA markers. The results showed that Pakistani landraces were more diverse than Iranian landraces. Genome-wide association study (GWAS) using climatic data identified 91 and 58 genomic regions for landraces from Iran and Pakistan, respectively, that were associated with climatic variation. Selective sweep analysis identified significant associations on six chromosomes, which were co-lozalized with the genes associated with flowering time and grain size. Information on the genetic diversity and local adaptation of these landraces may be useful in breeding cultivars that are well adapted to particular environments.

Technical Abstract: Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The minor allele frequency (MAF) and the heterozygosity of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightlty higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightlty more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, indicating two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as reveleaed by the correlation coefficients. Genome-wide association study (GWAS) identified 91 and 58 loci, using agroclimatic data, which likely underpin local adaptability of the wheat landraces. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were co-lozalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.