Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population

Waltram Ravelombola,Huda Alshaya,Bazgha Zia,Dotun Olaoye,Bao-Lam Huynh,Aurora Manley,Ibtisam Alatawi,Lingdi Dong,Ainong Shi,Gehendra Bhattarai,Haizheng Xiong,Jun Qin

doi:10.1186/s12864-022-08332-y

Abstract

BackgroundPrevious reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in cowpea. Phenotyping was validated through the use of salt-tolerant and salt-susceptible controls that were previously reported. Genome-wide association study (GWAS) was conducted using a total of 32,047 filtered SNPs. The epistatic interaction analysis was conducted using the PLINK platform.ResultsResults indicated that: (1) large variation in traits evaluated for salt tolerance was identified among the MAGIC lines, (2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 were associated with number of dead plants, salt injury score, leaf SPAD chlorophyll under salt treatment, relative tolerance index for leaf SPAD chlorophyll, fresh leaf biomass under salt treatment, relative tolerance index for fresh leaf biomass, relative tolerance index for fresh stem biomass, relative tolerance index for the total above-ground fresh biomass, and relative tolerance index for plant height, respectively, with overlapping SNP markers between traits, (3) candidate genes encoding for proteins involved in ion transport such as Na+/Ca2+ K+ independent exchanger and H+/oligopeptide symporter were identified, and (4) epistatic interactions were identified.ConclusionsThese results will have direct applications in breeding programs aiming at improving salt tolerance in cowpea through marker-assisted selection. To the best of our knowledge, this study was one of the earliest reports using a MAGIC population to investigate the genetic architecture of salt tolerance in cowpea.

Highlights

Previous reports have shown that soil salinity is a growing threat to cowpea production, and the need for breeding salt-tolerant cowpea cultivars
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A significant difference in the average number of dead plants per pot was found among the lines (F-value=15.3, p-value

Summary

Introduction

Previous reports have shown that soil salinity is a growing threat to cowpea production, and the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt toler‐ ance in cowpea. Cowpea is a legume that has a multipurpose use. It provides an excellent and affordable source of protein to human [4]. The significant amount of antioxidant compounds within cowpea seeds provides additional nutritional value that would be of interest when incorporated into the diet [6, 7]. With its excellent root architecture plus nitrogen fixation, cowpea can be used as a cover crop that has attracted considerable attention in recent years [8]

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