Yuejin Weng

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

Abstract: Cowpea (Vigna unguiculata L. Walp.) is an important legume, and the antioxidant content in cowpea seeds has been recognized as a health-promoting compound for humans. The objectives of this study were to analyze the population structure of cowpea collections and to identify single nucleotide polymorphism (SNP) markers associated with the seed antioxidant content and seed coat colour. A set of 1047 SNPs were used to analyze a 369 cowpea core collection from 47 countries. Results indicated that: (1) there were three clusters in the 369 entries; and the germplasm collected from India, South Africa, and the US showed broader genetic diversity; (2) Scaffold7139_14363 and Scaffold29110_4657 were strongly associated with antioxidant content, and C35063613_1497, Scaffold81493_886, and Scaffold84620_6785 were strongly associated with seed coat colour across three models; (3) significant correlations were detected between the seed antioxidant content and black seed colour (r = 0.45) and between seed antioxidant content and red seed coat colour (r = 0.50); and (4) Scaffold42008_191 and C35082838_2258 were associated with both seed antioxidant content and seed coat colour. The SNP markers identified could potentially be used in marker-assisted breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content.

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.

Genome-Wide Identification, Classification and Evolutionary Expansion of KNOX Gene Family in Rice ( Oryza sativa ) and Populus ( Populustrichocarpa )

The KNOX gene family codes for transcriptional regulators with a variety of functions in plant developmental and physiological processes. In this study, a genome-wide comparative analysis of KNOX genes in Poplar (Populustrichocarpa) and rice (Oryza sativa L. ssp. japonica) was carried out. With comprehensive computational analyses, which take into account the gene structures, phylogeny and conserved motifs, 15 and 13 KNOX genes in Poplar and rice were identified, respectively. These KNOX genes were further divided into 3 groups. The Poplar gene POPTR_0012s04040 and the rice genes LOC_Os03g47042 and LOC_Os03g47022 were classified to a new group of KNOX genes without ahomeobox domain together with KNATM, which were proposed to play potential role in plant development and pluripotency. The identification of KNATM homolog in monocotyledons (rice) provided a strong support for proposing an ancient shuffling of HOMEOBOX gene with MEINOX gene took place in the KNOX phylogeny. Using subcellular location information, GO (gene ontology) and expression profile analysis, KNOX genes in rice and poplar were proposed to function similarly to the members in Arabidopsis. Our observations may lay the foundation for future functional analysis of KNOX genes in rice and poplar to unravel their biological roles in cellular pluripotency.

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.