Waltram Ravelombola

Association mapping revealed SNP markers for adaptation to low phosphorus conditions and rock phosphate response in USDA cowpea ( Vigna unguiculata (L.) Walp.) germplasm

Cowpea (Vigna unguiculata (L.) Walp) is a legume of economic importance world-wide, especially in Western Africa, where it is an important part of the population’s diet. The rapidly increasing population growth in Africa requires substantial increase in cowpea production, which can be achieved by expanding land areas for agricultural purposes. In addition, prevalence of soil acidity in Africa constrains such an alternative since phosphorus availability, a key element for plant growth and development, is limited, thus resulting in poor cowpea production. The objectives of this study were to conduct an association analysis for adaptation to low phosphorus conditions and rock phosphate response in cowpea, and to identify SNP markers associated with these two traits. A total of 357 cowpea accessions, collected worldwide, was evaluated for phosphorus stress and response to addition of rock phosphate. Association analysis was conducted using 1018 SNPs obtained using genotyping-by-sequencing (GBS). TASSEL 5 and R were used for association mapping studies based on six different models. The results indicated that: (1) substantial variability in adaptation to low phosphorus conditions and rock phosphate response exists in the USDA cowpea accession panel; (2) ten SNP markers, C35006753_110, C35028233_482, C35072764_1384, C35084634_455, Scaffold21750_4938, Scaffold26894_5408, Scaffold41885_14420, Scaffold45170_4650, Scaffold50732_679; and Scaffold88448_741 were found to be associated with tolerance to low phosphorus conditions in cowpea, and (3) eight SNP markers, C35028233_482, C35058535_121, Scaffold26894_5408, Scaffold45170_4650, Scaffold51609_507, Scaffold53730_7339, Scaffold74389_5733, and Scaffold87916_4921 were highly associated with rock phosphate response. These SNP markers can be used in a marker-assisted breeding (MAS) program to improve cowpea tolerance to phosphorus stress.

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

BackgroundSpinach 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.ResultsA 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.ConclusionsThe 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.

Population structure analysis and association mapping for iron deficiency chlorosis in worldwide cowpea (Vigna unguiculata (L.) Walp) germplasm

Cowpea (Vigna unguiculata L. Walp) is a legume consumed for its high protein content. It provides nutrient-dense food opportunities for human consumption. Iron deficiency chlorosis (IDC) manifests as yellowing of the leaves and reduced plant growth, resulting in reduced yield potential. Use of IDC tolerant cowpea cultivars is an efficient method to address this problem. The objectives of this study were to conduct a population structure analysis, to carry out an association mapping study, and to identify SNP markers associated with IDC tolerance in cowpea. A total of 353 cowpea accessions were evaluated for tolerance/susceptibly to low soluble iron conditions on higher pH soils. A total of 1006 SNP markers postulated from genotyping-by-sequencing were used after filtering for population structure and association analysis studies. Results revealed that: (1) a substantial variability in degree of tolerance to low soluble iron conditions was found among the cowpea accessions; (2) delta K peak was identified at K equal to 2, indicating two subpopulations within the cowpea accessions tested for adaptation to IDC, a second delta peak corresponding to K equal to 3 was also found; and (3) nine SNP markers, C35081162_3130, Scaffold16136_2033, Scaffold1764_4741, Scaffold18262_4480, Scaffold30165_15499, Scaffold47194_5530, Scaffold73235_6677, Scaffold77932_9959, and Scaffold86559_7193, were significantly associated with IDC tolerance in cowpea. These results can be used as tools to select cowpea genotypes tolerant to IDC under low soluble iron conditions.

Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing.

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs.

A SNP-based association analysis for plant growth habit in worldwide cowpea ( Vigna unguiculata (L.) Walp) Germplasm

Cowpea is a legume widely grown in Africa, North, Central and South America, and Asia. The cowpea plant growth habits consist of erect, semi-prostrate, and prostrate types. Developing a cultivar while considering plant growth habit is essential within a breeding program since the need for a particular growth habit is region-specific, and significantly depends on the end user preference. Some cowpea growers might prefer erect types over semi-prostrate and prostrate types, while others would chose prostrate types, which provide more leaves for feed supplies to livestock. However, very little is known regarding the genetics of plant growth habit in cowpea to assist plant breeders in developing suitable cowpea cultivars having the desired growth habit plus the other required features. Therefore, the objectives of this study were to conduct an association mapping for cowpea growth habit, and to identify SNP markers associated with this trait. A total of 487 cowpea genotypes were evaluated for growth habit and a total of 1031 SNPs postulated from genotyping-by-sequencing to conduct association analysis study for cowpea growth habit. Our results showed that: (1) significant differences in cowpea growth habit were identified between countries, (2) the cowpea erect-type was prevalent, and (3) ten SNP markers, C35060651_729, C35061339_799, C35062457_1855, C35072764_1384, C35080248_2355, Scaffold2771_4351, Scaffold29522_3213, Scaffold35913_2678, Scaffold53560_188, and Scaffold58098_4297, were significantly associated with cowpea growth habit. These results could be used for enhancing marker-assisted selection (MAS) in breeding programs aimed at developing cowpea cultivars having a particular growth habit.

Association analysis of cowpea mosaic virus (CPMV) resistance in the USDA cowpea germplasm collection

Cowpea [Vigna unguiculata (L.) Walp.] is an important legume crop, widely grown in Africa, South America, South Asia, Southeast Asia, and the southern United States. Cowpea is consumed as both fresh vegetable and dry grain, and as an animal feed and fodder, and it is a major dietary protein source that complements cereal-based diet. Cowpea mosaic virus (CPMV) causes a severe yield loss of cowpea in many areas worldwide notably in the Africa. Utilization of host genetic resistance is the most effective control method for the viral disease. The objective of this research is to conduct genome-wide association analysis and identify single nucleotide polymorphism (SNP) markers associated with CPMV resistance in cowpea. Three hundred and thirty-three cowpea germplasm accessions, originally collected from 39 different countries and 1033 SNPs identified from genotyping by sequencing approach were used in this study. Single marker regression, general linear model, and mixed linear model in Tassel 5 were used for association analysis of CPMV resistance. Six SNP markers (C35069548_1883, scaffold65342_6794, scaffold66293_6549, scaffold95805_2175, C35081948_540, and scaffold17319_4417) were strongly associated with the CPMV resistance, of which the first three were associated for immune and the remaining three were associated with hypersensitive response. SNP markers identified in this research will be a potential tool to use in cowpea molecular breeding to develop CPMV resistant cultivars through marker-assisted selection.