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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #340953
Title: Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages

Author
item RAVELOMBOLA, SECOND WALTRAM - University Of Arkansas
item SHI, AINONG - University Of Arkansas
item WENG, YUEJIN - University Of Arkansas
item Mou, Beiquan
item MOTES, DENNIS - University Of Arkansas
item CLARK, JOHN - University Of Arkansas
item CHEN, PENGYIN - University Of Missouri
item SRIVASTAVA, VIBHA - University Of Arkansas
item QIN, JUN - University Of Arkansas
item DONG, LINGDI - University Of Arkansas
item YANG, WEI - University Of Arkansas
item BHATTARAI, GEHENDRA - University Of Arkansas
item SUGIHARA, YUICHI - University Of Arkansas

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/30/2017
Publication Date: 1/1/2018
Citation: Ravelombola, S., Shi, A., Weng, Y., Mou, B., Motes, D., Clark, J., Chen, P., Srivastava, V., Qin, J., Dong, L., Yang, W., Bhattarai, G., Sugihara, Y. 2018. Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages. Theoretical and Applied Genetics. 131(1):79-91. https://doi.org/10.1007/s00122-017-2987-0.
DOI: https://doi.org/10.1007/s00122-017-2987-0

Interpretive Summary: Cowpea is one of the most consumed legumes worldwide, especially in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetics underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt tolerant cowpea cultivars. The objectives of this work were to study salt tolerance at germination and seedling stages and to identify molecular markers associated with salt tolerance in cowpea. We analyzed the salt tolerance of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1,049 molecular markers were identified by DNA sequencing. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were divided into two subpopulations. Three molecular markers were found to be associated with salt tolerance at germination stage. Seven molecular markers were associated with salt tolerance at seedling stage. The molecular markers identified could be used as a tool to select salt-tolerant plants for breeding improved cowpea cultivars with tolerance to salinity.

Technical Abstract: Cowpea is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1,049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structure 2.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression (SMR), general linear model (GLM), and mixed linear model (MLM) were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.