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. 2021 Nov 26;12(12):1897.
doi: 10.3390/genes12121897.

Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Endale G Tafesse  1 , Krishna K Gali  1 , V B Reddy Lachagari  2 , Rosalind Bueckert  1 , Thomas D Warkentin  1
Affiliations

Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Endale G Tafesse et al. Genes (Basel). .

Abstract

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

Keywords: drought; genome-wide association study; genotyping-by-sequencing; heat; marker–trait association; pea; stress.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Box plots of lamina wax, petiole wax, stem thickness, flowering duration, normalized difference vegetation index (NDVI), and normalized pigment and chlorophyll index (NPCI) of 135 pea accessions grown under control and stress conditions across multiple environments in Saskatchewan, Canada. Note: The control environments were 2016 Rosthern, 2016 Saskatoon, and 2017 Rosthern; the stress environments were 2015 and 2017 Saskatoon.
Figure 2
Figure 2
Bi-plot of principal component analysis depicting the overall traits association and accessions response to the environment. Note: The control environments were 2016 Rosthern, 2016 Saskatoon, and 2017 Rosthern; the stress environments were 2015 and 2017 Saskatoon. LWAX, lamina wax; PWAX, petiole wax; ST, stem thickness, FD, flowering duration; NDVI, normalized difference vegetation index, and NPCI, normalized pigment and chlorophyll index.
Figure 3
Figure 3
Manhattan plots and the corresponding Q-Q plots displaying the p values of the identified SNP markers to be associated with lamina wax (A), petiole wax (B), stem thickness (C), flowering duration (D), normalized difference vegetation index (E), and normalized pigment and chlorophyll index (F). The Manhattan plots are determined using a total of 16,877 SNP markers of 135 pea accessions in the multi-environment experiments.
See this image and copyright information in PMC

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