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  • 1
    Online Resource
    Online Resource
    Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance
    Springer Science and Business Media LLC ; 2019
    In:  BMC Genomics Vol. 20, No. 1 ( 2019-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2019-12)
    Abstract: Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance. Results A total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN. Conclusions In this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-019-6275-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2041499-7
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  • 2
    Online Resource
    Online Resource
    Data_Sheet_2.xlsx
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-6-16)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-6-16)
    Abstract: Soybean is a primary meal protein for human consumption, poultry, and livestock feed. In this study, quantitative trait locus (QTL) controlling protein content was explored via genome-wide association studies (GWAS) and linkage mapping approaches based on 284 soybean accessions and 180 recombinant inbred lines (RILs), respectively, which were evaluated for protein content for 4 years. A total of 22 single nucleotide polymorphisms (SNPs) associated with protein content were detected using mixed linear model (MLM) and general linear model (GLM) methods in Tassel and 5 QTLs using Bayesian interval mapping (IM), single-trait multiple interval mapping (SMIM), single-trait composite interval mapping maximum likelihood estimation (SMLE), and single marker regression (SMR) models in Q-Gene and IciMapping. Major QTLs were detected on chromosomes 6 and 20 in both populations. The new QTL genomic region on chromosome 6 (Chr6_18844283–19315351) included 7 candidate genes and the Hap.X AA at the Chr6_19172961 position was associated with high protein content. Genomic selection (GS) of protein content was performed using Bayesian Lasso (BL) and ridge regression best linear unbiased prediction (rrBULP) based on all the SNPs and the SNPs significantly associated with protein content resulted from GWAS. The results showed that BL and rrBLUP performed similarly; GS accuracy was dependent on the SNP set and training population size. GS efficiency was higher for the SNPs derived from GWAS than random SNPs and reached a plateau when the number of markers was & gt;2,000. The SNP markers identified in this study and other information were essential in establishing an efficient marker-assisted selection (MAS) and GS pipelines for improving soybean protein content.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.882732
    DOI: 10.3389/fpls.2022.882732.s001
    DOI: 10.3389/fpls.2022.882732.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 3
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    Online Resource
    Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population
    Oxford University Press (OUP) ; 2021
    In:  Horticulture Research Vol. 8, No. 1 ( 2021-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 8, No. 1 ( 2021-12)
    Abstract: Cowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the drought tolerance index for plant growth habit, plant maturity, flowering time, 100-seed weight, and grain yield in a MAGIC cowpea population, to conduct genome-wide association study (GWAS) and identify single nucleotide polymorphism (SNP) markers associated with the drought tolerance indices, to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices, and to conduct genomic selection (GS). These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines (RILs) developed at University of California, Riverside. The results indicated that: (1) large variation in drought tolerance indices existed among the cowpea genotypes, (2) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, and drought tolerance indices for maturity, flowering time, 100-seed weight, and grain yield, respectively, (3) the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and (4) the GS accuracy varied from low to moderate. These results could be applied to improve drought tolerance in cowpea through marker-assisted selection (MAS) and genomic selection (GS). To the best of our knowledge, this is the first report on marker loci associated with drought tolerance indices in cowpea.
    Type of Medium: Online Resource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-021-00462-w
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2781828-7
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  • 4
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    Online Resource
    Genetic diversity and association mapping of mineral element concentrations in spinach leaves
    Springer Science and Business Media LLC ; 2017
    In:  BMC Genomics Vol. 18, No. 1 ( 2017-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-017-4297-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 5
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    Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population
    Springer Science and Business Media LLC ; 2022
    In:  BMC Genomics Vol. 23, No. 1 ( 2022-02-05)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-02-05)
    Abstract: Previous reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in cowpea. Phenotyping was validated through the use of salt-tolerant and salt-susceptible controls that were previously reported. Genome-wide association study (GWAS) was conducted using a total of 32,047 filtered SNPs. The epistatic interaction analysis was conducted using the PLINK platform. Results Results indicated that: (1) large variation in traits evaluated for salt tolerance was identified among the MAGIC lines, (2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 were associated with number of dead plants, salt injury score, leaf SPAD chlorophyll under salt treatment, relative tolerance index for leaf SPAD chlorophyll, fresh leaf biomass under salt treatment, relative tolerance index for fresh leaf biomass, relative tolerance index for fresh stem biomass, relative tolerance index for the total above-ground fresh biomass, and relative tolerance index for plant height, respectively, with overlapping SNP markers between traits, (3) candidate genes encoding for proteins involved in ion transport such as Na+/Ca2+ K+ independent exchanger and H+/oligopeptide symporter were identified, and (4) epistatic interactions were identified. Conclusions These results will have direct applications in breeding programs aiming at improving salt tolerance in cowpea through marker-assisted selection. To the best of our knowledge, this study was one of the earliest reports using a MAGIC population to investigate the genetic architecture of salt tolerance in cowpea.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-022-08332-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2041499-7
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  • 6
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    Online Resource
    Evaluation of Salt Tolerance at Germination Stage in Cowpea [Vigna unguiculata (L.) Walp]
    American Society for Horticultural Science ; 2017
    In:  HortScience Vol. 52, No. 9 ( 2017-09), p. 1168-1176
    Details
    In: HortScience, American Society for Horticultural Science, Vol. 52, No. 9 ( 2017-09), p. 1168-1176
    Abstract: Cowpea is a leguminous and versatile crop which provides nutritional food for human consumption. However, salinity unfavorably reduces cowpea seed germination, thus significantly decreasing cowpea production. Little has been done for evaluating and developing salt-tolerant cowpea genotypes at germination stage. The objectives of this research were to evaluate the response of cowpea genotypes to salinity stress through seed germination rate and to select salt-tolerant cowpea genotypes. The seed germination rates under nonsalt condition and salinity stress (150 m m NaCl) were evaluated in 151 cowpea genotypes. Four parameters, absolute decrease (AD), the inhibition index (II), the relative salt tolerance (RST), and the salt tolerance index (STI) were used to measure salt tolerance in cowpea. The results showed that there were significant differences among the 151 cowpea genotypes for all parameters ( P values 〈 0.0001). The AD in germination rate was 5.8% to 94.2%; the II varied from 7.7% to 100%; the RST ranged from 0 to 0.92; and STI varied from 0 to 0.92. A high broad sense heritability (H 2 ) was observed for all four parameters. High correlation coefficients (r) were estimated among the four parameters. PI582422, 09–529, PI293584, and PI582570 were highly salt tolerant at germination stage. In addition, genotypes from the Caribbean and Southern Asia exhibited better tolerance to salinity, whereas those from Europe and North America were the most salt-susceptible.
    Type of Medium: Online Resource
    ISSN: 0018-5345 , 2327-9834
    URL: Article
    DOI: 10.21273/HORTSCI12195-17
    Language: Unknown
    Publisher: American Society for Horticultural Science
    Publication Date: 2017
    detail.hit.zdb_id: 2040198-X
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  • 7
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    Online Resource
    Investigation on Various Aboveground Traits to Identify Drought Tolerance in Cowpea Seedlings
    American Society for Horticultural Science ; 2018
    In:  HortScience Vol. 53, No. 12 ( 2018-12), p. 1757-1765
    Details
    In: HortScience, American Society for Horticultural Science, Vol. 53, No. 12 ( 2018-12), p. 1757-1765
    Abstract: 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 plant morphology 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 plant morphology 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.
    Type of Medium: Online Resource
    ISSN: 0018-5345 , 2327-9834
    URL: Article
    DOI: 10.21273/HORTSCI13278-18
    Language: Unknown
    Publisher: American Society for Horticultural Science
    Publication Date: 2018
    detail.hit.zdb_id: 2040198-X
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  • 8
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    Online Resource
    Use of Unmanned Aerial System (UAS) Phenotyping to Predict Pod and Seed Yield in Organic Peanuts
    Scientific Research Publishing, Inc. ; 2023
    In:  American Journal of Plant Sciences Vol. 14, No. 03 ( 2023), p. 415-426
    Details
    In: American Journal of Plant Sciences, Scientific Research Publishing, Inc., Vol. 14, No. 03 ( 2023), p. 415-426
    Type of Medium: Online Resource
    ISSN: 2158-2742 , 2158-2750
    URL: Article
    DOI: 10.4236/ajps.2023.143027
    Language: Unknown
    Publisher: Scientific Research Publishing, Inc.
    Publication Date: 2023
    detail.hit.zdb_id: 2635691-0
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  • 9
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    A Genome-Wide Association Study Reveals Region Associated with Seed Protein Content in Cowpea
    MDPI AG ; 2023
    In:  Plants Vol. 12, No. 14 ( 2023-07-20), p. 2705-
    Details
    In: Plants, MDPI AG, Vol. 12, No. 14 ( 2023-07-20), p. 2705-
    Abstract: Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock. It is widely grown in Africa and other developing countries as the primary source of protein in the diet; therefore, it is necessary to identify the protein-related loci to improve cowpea breeding. In the current study, we conducted a genome-wide association study (GWAS) on 161 cowpea accessions (151 USDA germplasm plus 10 Arkansas breeding lines) with a wide range of seed protein contents (21.8~28.9%) with 110,155 high-quality whole-genome single-nucleotide polymorphisms (SNPs) to identify markers associated with protein content, then performed genomic prediction (GP) for future breeding. A total of seven significant SNP markers were identified using five GWAS models (single-marker regression (SMR), the general linear model (GLM), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), which are located at the same locus on chromosome 8 for seed protein content. This locus was associated with the gene Vigun08g039200, which was annotated as the protein of the thioredoxin superfamily, playing a critical function for protein content increase and nutritional quality improvement. In this study, a genomic prediction (GP) approach was employed to assess the accuracy of predicting seed protein content in cowpea. The GP was conducted using cross-prediction with five models, namely ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL), applied to seven random whole genome marker sets with different densities (10 k, 5 k, 2 k, 1 k, 500, 200, and 7), as well as significant markers identified through GWAS. The accuracies of the GP varied between 42.9% and 52.1% across the seven SNPs considered, depending on the model used. These findings not only have the potential to expedite the breeding cycle through early prediction of individual performance prior to phenotyping, but also offer practical implications for cowpea breeding programs striving to enhance seed protein content and nutritional quality.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    URL: Article
    DOI: 10.3390/plants12142705
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2704341-1
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  • 10
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    A SNP-based association analysis for plant growth habit in worldwide cowpea (Vigna unguiculata (L.) Walp) Germplasm
    Springer Science and Business Media LLC ; 2017
    In:  Euphytica Vol. 213, No. 12 ( 2017-12)
    Details
    In: Euphytica, Springer Science and Business Media LLC, Vol. 213, No. 12 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 0014-2336 , 1573-5060
    URL: Article
    DOI: 10.1007/s10681-017-2077-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2012322-X
    SSG: 12
    SSG: 21
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