Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach
Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) is a diploid legume crop used for human consumption, feed for livestock, and cover crops. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genome-wide asso...
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MDPI AG
2023-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/20/15281 |
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| author | Waltram Ravelombola Lindgi Dong Thomas Casey Barickman Haizheng Xiong Aurora Manley John Cason Hanh Pham Bazgha Zia Beiquan Mou Ainong Shi |
| author_facet | Waltram Ravelombola Lindgi Dong Thomas Casey Barickman Haizheng Xiong Aurora Manley John Cason Hanh Pham Bazgha Zia Beiquan Mou Ainong Shi |
| author_sort | Waltram Ravelombola |
| collection | DOAJ |
| description | Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) is a diploid legume crop used for human consumption, feed for livestock, and cover crops. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify SNP markers and to investigate candidate genes for salt tolerance in cowpea. A total of 331 cowpea genotypes were evaluated for salt tolerance by supplying a solution of 200 mM NaCl in our previous work. The cowpea panel was genotyped using a whole genome resequencing approach, generating 14,465,516 SNPs. Moreover, 5,884,299 SNPs were used after SNP filtering. GWAS was conducted on a total of 296 cowpea genotypes that have high-quality SNPs. BLINK was used for conducting GWAS. Results showed (1) a strong GWAS peak on an 890-bk region of chromosome 2 for leaf SPAD chlorophyll under salt stress in cowpea and harboring a significant cluster of nicotinamide adenine dinucleotide (NAD) dependent epimerase/dehydratase genes such as <i>Vigun02g128900.1</i>, <i>Vigun02g129000.1</i>, <i>Vigun02g129100.1</i>, <i>Vigun02g129200.1</i>, and <i>Vigun02g129500.1</i>; (2) two GWAS peaks associated with relative tolerance index for chlorophyll were identified on chromosomes 1 and 2. The peak on chromosome 1 was defined by a cluster of 10 significant SNPs mapped on a 5 kb region and was located in the vicinity of <i>Vigun01g086000.1</i>, encoding for a GATA transcription factor. The GWAS peak on chromosome 2 was defined by a cluster of 53 significant SNPs and mapped on a 68 bk region of chromosome 2, and (3) the highest GWAS peak was identified on chromosome 3, and this locus was associated with leaf score injury. This peak was within the structure of a potassium channel gene (<i>Vigun03g144700.1</i>). To the best of our knowledge, this is one the earliest reports on the salt tolerance study of cowpea using whole genome resequencing data. |
| first_indexed | 2024-03-10T21:11:27Z |
| format | Article |
| id | doaj.art-14127f30483a41a2a5762c55524f8cb4 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T21:11:27Z |
| publishDate | 2023-10-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-14127f30483a41a2a5762c55524f8cb42023-11-19T16:44:24ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-10-0124201528110.3390/ijms242015281Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing ApproachWaltram Ravelombola0Lindgi Dong1Thomas Casey Barickman2Haizheng Xiong3Aurora Manley4John Cason5Hanh Pham6Bazgha Zia7Beiquan Mou8Ainong Shi9Texas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USAInstitute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, ChinaNorth Mississippi Research and Extension Center, Department of Plant and Soil Sciences, Mississippi State University, Verona, MS 38879, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USATexas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USATexas A&M AgriLife Research, 1129 North US Highway 281, Stephenville, TX 76401, USATexas A&M AgriLife Research, 1102 East Drew Street, Lubbock, TX 79403, USAUnited States Vegetable Lab (USVL), 2700 Savannah Hwy, Charleston, SC 29414, USAAgricultural Research Service (USDA ARS), 1636 E. Alisal St., Salinas, CA 93905, USADepartment of Horticulture, University of Arkansas, Fayetteville, AR 72701, USACowpea (<i>Vigna unguiculata</i> (L.) Walp.) is a diploid legume crop used for human consumption, feed for livestock, and cover crops. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify SNP markers and to investigate candidate genes for salt tolerance in cowpea. A total of 331 cowpea genotypes were evaluated for salt tolerance by supplying a solution of 200 mM NaCl in our previous work. The cowpea panel was genotyped using a whole genome resequencing approach, generating 14,465,516 SNPs. Moreover, 5,884,299 SNPs were used after SNP filtering. GWAS was conducted on a total of 296 cowpea genotypes that have high-quality SNPs. BLINK was used for conducting GWAS. Results showed (1) a strong GWAS peak on an 890-bk region of chromosome 2 for leaf SPAD chlorophyll under salt stress in cowpea and harboring a significant cluster of nicotinamide adenine dinucleotide (NAD) dependent epimerase/dehydratase genes such as <i>Vigun02g128900.1</i>, <i>Vigun02g129000.1</i>, <i>Vigun02g129100.1</i>, <i>Vigun02g129200.1</i>, and <i>Vigun02g129500.1</i>; (2) two GWAS peaks associated with relative tolerance index for chlorophyll were identified on chromosomes 1 and 2. The peak on chromosome 1 was defined by a cluster of 10 significant SNPs mapped on a 5 kb region and was located in the vicinity of <i>Vigun01g086000.1</i>, encoding for a GATA transcription factor. The GWAS peak on chromosome 2 was defined by a cluster of 53 significant SNPs and mapped on a 68 bk region of chromosome 2, and (3) the highest GWAS peak was identified on chromosome 3, and this locus was associated with leaf score injury. This peak was within the structure of a potassium channel gene (<i>Vigun03g144700.1</i>). To the best of our knowledge, this is one the earliest reports on the salt tolerance study of cowpea using whole genome resequencing data.https://www.mdpi.com/1422-0067/24/20/15281cowpeaseedlingsaltGWASwhole genome |
| spellingShingle | Waltram Ravelombola Lindgi Dong Thomas Casey Barickman Haizheng Xiong Aurora Manley John Cason Hanh Pham Bazgha Zia Beiquan Mou Ainong Shi Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach International Journal of Molecular Sciences cowpea seedling salt GWAS whole genome |
| title | Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach |
| title_full | Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach |
| title_fullStr | Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach |
| title_full_unstemmed | Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach |
| title_short | Genetic Architecture of Salt Tolerance in Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach |
| title_sort | genetic architecture of salt tolerance in cowpea i vigna unguiculata i l walp at seedling stage using a whole genome resequencing approach |
| topic | cowpea seedling salt GWAS whole genome |
| url | https://www.mdpi.com/1422-0067/24/20/15281 |
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