Genetic Architecture of Salt and Drought Tolerance in Cowpea

Cowpea [Vigna unguiculata (L.) Walp.] is a diploid and nutrient-dense legume species. It provides affordable source of protein to human. Cowpea cultivation is prevalent in Africa, Asia, the western and southern U.S., and Central and South America. However, earlier reports have shown that drought and salt stress can be devastating to cowpea production. The objectives of this study were to screen for salt and drought tolerance in cowpea and to identify molecular markers associated with these traits. Simple methodologies to screen for drought (Chapter 2) and salt tolerance were developed (Chapter 3). Results suggested that: 1) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, drought tolerance index for maturity, flowering time, 100-seed weight, and grain yield respectively in a MAGIC cowpea population, the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and GS accuracy varied from low to moderate for this population, 2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 SNPs were associated with various traits evaluated for salt tolerance in a MAGIC cowpea population, some of these SNPs were in the vicinity of potassium channel and biomolecule transporters, and significant epistatic interactions were found 3) a large variation of salt tolerance and drought tolerance was found in the panel involving 331 cowpea genotypes which were genotyped with 14,465,516 SNPs obtained from whole-genome resequencing, 4) tolerance to salt and drought-related traits seemed to be associated with the geographical origins of the cowpea genotypes, 5) a significant GWAS peak defined by a cluster of 196 significant SNPs and mapped on a 210-kb region of chromosome 5 was identified to be a good locus candidate for tolerance to trifoliate leaf chlorosis under drought stress in cowpea and harbored hormone-induced genes, and 6) a strong candidate locus for tolerance to leaf score injury under salt stress and defined by a cluster of 1,400 significant SNPs on chromosome 3 was identified and this region harbored a potassium channel gene. The results from this study could contribute to a better understanding of salt and drought tolerance in cowpea. The salt- and drought-tolerant genotypes could be used as parents in cowpea breeding programs

Evaluation and Association Analysis of Cowpea Salt Tolerance

Cowpea [Vigna unguiculata (L.) Walp.] (2n=2x=22) is a leguminous crop providing inexpensive protein for human consumption that can be grown worldwide. Salinity is one of the major threats to cowpea production, particularly in semi-arid regions of Africa. Salinity significantly affects seed germination and decreases pod yield in cowpea. However, little has been done to provide farmers salt-tolerant cowpea cultivars. Knowledge on the genetics of cowpea salt tolerance is very limited. This study aimed to:(1) evaluate cowpea salt tolerance at germination stage, (2) evaluate cowpea salt tolerance at seedling stage, (3) conduct an association study for cowpea salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. A total of 151 cowpea genotypes at germination stage and 203 cowpea genotypes at seedling stage were evaluated in this research. Association analysis was performed on 116 genotypes at germination stage and 155 genotypes at seedling stage. The results indicated that: (1) substantial variability in salt tolerance was found among the tested cowpea genotypes at both germination and seedling stages; (2) three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage; (3) 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, and (4) PI582422, 09-529, PI293584, and PI582570 were highly salt tolerant at germination stage, and PI293570, PI582812, PI582856, PI180014, PI257463, 09-175, 09-529, PI666260, I582402, and PI582340 were highly salt tolerant at seedling stage. This research will have practical applications in cowpea breeding and genetics. The salt tolerant lines could be used as parents for breeding programs and the SNP markers could be used as a tools in cowpea molecular breeding through marker-assisted selection

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Impacts of drought stress on crop production can significantly impair farmer’s revenue, hence adversely impacting the gross national product growth. For cowpea [Vigna unguiculata (L.) Walp.], which is a legume of economic importance, effects of drought at early vegetative growth could lead to substantial yield losses. However, little has been done with respect to breeding for cowpea cultivars withstanding drought at early vegetative growth. In addition, previous investigations have focused on how plantmorphology and root architecture can confer drought tolerance in cowpea, which is not sufficient in efforts to unravel unknown drought tolerance–related genetic mechanisms, potentially of great importance in breeding, and not pertaining to either plantmorphology or root architecture. Therefore, the objective of this study was to evaluate aboveground drought-related traits of cowpea genotypes at seedling stage. A total of 30 cowpea genotypes were greenhouse grown within boxes and the experimental design was completely randomized with three replicates. Drought stress was imposed for 28 days. Data on a total of 17 aboveground-related traits were collected. Results showed the following: 1) a large variation in these traits was found among the genotypes; 2) more trifoliate wilt/chlorosis tolerance but more unifoliate wilt/chlorosis susceptible were observed; 3) delayed senescence was related to the ability of maintaining a balanced chlorophyll content in both unifoliate and trifoliate leaves; and 4) the genotypes PI293469, PI349674, and PI293568 were found to be slow wilting and drought tolerant. These results could contribute to advancing breeding programs for drought tolerance in cowpea

Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings

Impacts of drought stress on crop production can significantly impair farmer’s revenue, hence adversely impacting the gross national product growth. For cowpea [Vigna unguiculata (L.) Walp.], which is a legume of economic importance, effects of drought at early vegetative growth could lead to substantial yield losses. However, little has been done with respect to breeding for cowpea cultivars withstanding drought at early vegetative growth. In addition, previous investigations have focused on how plantmorphology and root architecture can confer drought tolerance in cowpea, which is not sufficient in efforts to unravel unknown drought tolerance–related genetic mechanisms, potentially of great importance in breeding, and not pertaining to either plantmorphology or root architecture. Therefore, the objective of this study was to evaluate aboveground drought-related traits of cowpea genotypes at seedling stage. A total of 30 cowpea genotypes were greenhouse grown within boxes and the experimental design was completely randomized with three replicates. Drought stress was imposed for 28 days. Data on a total of 17 aboveground-related traits were collected. Results showed the following: 1) a large variation in these traits was found among the genotypes; 2) more trifoliate wilt/chlorosis tolerance but more unifoliate wilt/chlorosis susceptible were observed; 3) delayed senescence was related to the ability of maintaining a balanced chlorophyll content in both unifoliate and trifoliate leaves; and 4) the genotypes PI293469, PI349674, and PI293568 were found to be slow wilting and drought tolerant. These results could contribute to advancing breeding programs for drought tolerance in cowpea

Genetic diversity and association mapping of mineral element concentrations in spinach leaves

Abstract Background Spinach is a useful source of dietary vitamins and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorphism (SNP) markers for mineral element concentrations is necessary to support spinach molecular breeding. The purpose of this study was to conduct a genome-wide association study (GWAS) and to identify SNP markers associated with mineral elements in the USDA-GRIN spinach germplasm collection. Results A total of 14 mineral elements: boron (B), calcium (Ca), cobalt (Co), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), sodium (Na), nickel (Ni), phosphorus (P), sulfur (S), and zinc (Zn) were evaluated in 292 spinach accessions originally collected from 29 countries. Significant genetic variations were found among the tested genotypes as evidenced by the 2 to 42 times difference in mineral concentrations. A total of 2402 SNPs identified from genotyping by sequencing (GBS) approach were used for genetic diversity and GWAS. Six statistical methods were used for association analysis. Forty-five SNP markers were identified to be strongly associated with the concentrations of 13 mineral elements. Only two weakly associated SNP markers were associated with K concentration. Co-localized SNPs for different elemental concentrations were discovered in this research. Three SNP markers, AYZV02017731_40, AYZV02094133_57, and AYZV02281036_185 were identified to be associated with concentrations of four mineral components, Co, Mn, S, and Zn. There is a high validating correlation coefficient with r > 0.7 among concentrations of the four elements. Thirty-one spinach accessions, which rank in the top three highest concentrations in each of the 14 mineral elements, were identified as potential parents for spinach breeding programs in the future. Conclusions The 45 SNP markers strongly associated with the concentrations of the 13 mineral elements: B, Ca, Co, Cu, Fe, Mg, Mn, Mo, Na, Ni, P, S, and Zn could be used in breeding programs to improve the nutritional quality of spinach through marker-assisted selection (MAS). The 31 spinach accessions with high concentrations of one to several mineral elements can be used as potential parents for spinach breeding programs

Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation.

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance

Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

28 février 19371937/02/28 (A38,N13222)