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  • 1
    Online Resource
    Online Resource
    DataSheet2.xlsx
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-5-31)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-5-31)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2022.853114
    DOI: 10.3389/fgene.2022.853114.s001
    DOI: 10.3389/fgene.2022.853114.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 2
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    A Genome-Wide Association Study and Genomic Prediction for Fiber and Sucrose Contents in a Mapping Population of LCP 85-384 Sugarcane
    MDPI AG ; 2023
    In:  Plants Vol. 12, No. 5 ( 2023-02-24), p. 1041-
    Details
    In: Plants, MDPI AG, Vol. 12, No. 5 ( 2023-02-24), p. 1041-
    Abstract: Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the time and cost of developing new sugarcane varieties. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify DNA markers associated with fiber and sucrose contents and to perform genomic prediction (GP) for the two traits. Fiber and sucrose data were collected from 237 self-pollinated progenies of LCP 85-384, the most popular Louisiana sugarcane cultivar from 1999 to 2007. The GWAS was performed using 1310 polymorphic DNA marker alleles with three models of TASSEL 5, single marker regression (SMR), general linear model (GLM) and mixed linear model (MLM), and the fixed and random model circulating probability unification (FarmCPU) of R package. The results showed that 13 and 9 markers were associated with fiber and sucrose contents, respectively. The GP was performed by cross-prediction with five models, 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). The accuracy of GP varied from 55.8% to 58.9% for fiber content and 54.6% to 57.2% for sucrose content. Upon validation, these markers can be applied in MAS and genomic selection (GS) to select superior sugarcane with good fiber and high sucrose contents.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    URL: Article
    DOI: 10.3390/plants12051041
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2704341-1
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  • 3
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    Evaluation of salt tolerance in cowpea at seedling stage
    Springer Science and Business Media LLC ; 2021
    In:  Euphytica Vol. 217, No. 6 ( 2021-06)
    Details
    In: Euphytica, Springer Science and Business Media LLC, Vol. 217, No. 6 ( 2021-06)
    Type of Medium: Online Resource
    ISSN: 0014-2336 , 1573-5060
    URL: Article
    DOI: 10.1007/s10681-021-02832-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2012322-X
    SSG: 12
    SSG: 21
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  • 4
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    Revealing the role of the amorphous phase in Na0.74CoO2/C/N composite cathode
    Elsevier BV ; 2020
    In:  Journal of Alloys and Compounds Vol. 815 ( 2020-01), p. 152616-
    Details
    In: Journal of Alloys and Compounds, Elsevier BV, Vol. 815 ( 2020-01), p. 152616-
    Type of Medium: Online Resource
    ISSN: 0925-8388
    URL: Article
    DOI: 10.1016/j.jallcom.2019.152616
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
    detail.hit.zdb_id: 2012675-X
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  • 5
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    Physicochemical characterizations of starches isolated from Tetrastigma hemsleyanum Diels et Gilg
    Elsevier BV ; 2021
    In:  International Journal of Biological Macromolecules Vol. 183 ( 2021-07), p. 1540-1547
    Details
    In: International Journal of Biological Macromolecules, Elsevier BV, Vol. 183 ( 2021-07), p. 1540-1547
    Type of Medium: Online Resource
    ISSN: 0141-8130
    URL: Article
    DOI: 10.1016/j.ijbiomac.2021.05.117
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 1483284-7
    SSG: 12
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  • 6
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    Table_8.xlsx
    Frontiers Media SA ; 2023
    In:  Frontiers in Plant Science Vol. 14 ( 2023-5-29)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 14 ( 2023-5-29)
    Abstract: Soybean brown rust (SBR), caused by Phakopsora pachyrhizi , is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets. Four SNPs, namely Gm18_57,223,391 (LOD = 2.69), Gm16_29,491,946 (LOD = 3.86), Gm06_45,035,185 (LOD = 4.74), and Gm18_51,994,200 (LOD = 3.60), were located near the reported P. pachyrhizi R genes, Rpp1, Rpp2, Rpp3, and Rpp4, respectively. Other significant SNPs, including Gm02_7,235,181 (LOD = 7.91), Gm02_7234594 (LOD = 7.61), Gm03_38,913,029 (LOD = 6.85), Gm04_46,003,059 (LOD = 6.03), Gm09_1,951,644 (LOD = 10.07), Gm10_39,142,024 (LOD = 7.12), Gm12_28,136,735 (LOD = 7.03), Gm13_16,350,701(LOD = 5.63), Gm14_6,185,611 (LOD = 5.51), and Gm19_44,734,953 (LOD = 6.02), were associated with abundant disease resistance genes, such as Glyma.02G084100 , Glyma.03G175300 , Glyma.04g189500 , Glyma.09G023800 , Glyma.12G160400 , Glyma.13G064500 , Glyma.14g073300 , and Glyma.19G190200 . The annotations of these genes included but not limited to: LRR class gene, cytochrome 450 , cell wall structure, RCC1, NAC, ABC transporter, F-box domain, etc. The GWAS based markers showed more accuracies in genomic prediction than the whole genome SNPs, and Bayesian LASSO model was the ideal model in SBR resistance prediction with 44.5% ~ 60.4% accuracies. This study aids breeders in predicting selection accuracy of complex traits such as disease resistance and can shorten the soybean breeding cycle by the identified markers
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2023.1179357
    DOI: 10.3389/fpls.2023.1179357.s001
    DOI: 10.3389/fpls.2023.1179357.s002
    DOI: 10.3389/fpls.2023.1179357.s003
    DOI: 10.3389/fpls.2023.1179357.s004
    DOI: 10.3389/fpls.2023.1179357.s005
    DOI: 10.3389/fpls.2023.1179357.s006
    DOI: 10.3389/fpls.2023.1179357.s007
    DOI: 10.3389/fpls.2023.1179357.s008
    DOI: 10.3389/fpls.2023.1179357.s009
    DOI: 10.3389/fpls.2023.1179357.s010
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 7
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    Impact of nutrient solutions under inorganic substrate soilless cultivation on plant growth, fruit yield and quality of tomato
    Maximum Academic Press ; 2022
    In:  Technology in Horticulture Vol. 2, No. 1 ( 2022), p. 1-11
    Details
    In: Technology in Horticulture, Maximum Academic Press, Vol. 2, No. 1 ( 2022), p. 1-11
    Type of Medium: Online Resource
    ISSN: 2833-4337
    URL: Article
    DOI: 10.48130/TIH-2022-0005
    Language: Unknown
    Publisher: Maximum Academic Press
    Publication Date: 2022
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  • 8
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    Evaluation of Drought Tolerance in Arkansas Cowpea Lines at Seedling Stage
    American Society for Horticultural Science ; 2020
    In:  HortScience Vol. 55, No. 7 ( 2020-07), p. 1132-1143
    Details
    In: HortScience, American Society for Horticultural Science, Vol. 55, No. 7 ( 2020-07), p. 1132-1143
    Abstract: Cowpea [ Vigna unguiculate (L.) Walp.] is not only a healthy, nutritious, and versatile leguminous crop; it also has a relatively high adaptation to drought. Research has shown that cowpea lines have a high tolerance to drought, and many of them can survive more than 40 days under scorching and dry conditions. The cowpea (Southern pea) breeding program at the University of Arkansas has been active for more than 50 years and has produced more than 1000 advanced breeding lines. The purpose of this study was to evaluate the drought-tolerant ability in Arkansas cowpea lines and use the drought-tolerant lines in cowpea production or as parents in cowpea breeding. A total of 36 University of Arkansas breeding lines were used to screen drought tolerance at the seedling stage in this study. The experiment was conducted in the greenhouse using a randomized complete block design (RCBD) with two replicates, organized in a split-plot manner, where the drought treatment (drought and nondrought stress) as the main plot and the cowpea genotypes as the subplot. Drought stress was applied for 4 weeks, and three drought-tolerant–related traits were collected and analyzed. Results showed that cowpea breeding lines: ‘17-61’, ‘17-86’, ‘Early Scarlet’, and ‘ARBlackeye #1’ were found to be drought tolerant.
    Type of Medium: Online Resource
    ISSN: 0018-5345 , 2327-9834
    URL: Article
    DOI: 10.21273/HORTSCI15036-20
    Language: Unknown
    Publisher: American Society for Horticultural Science
    Publication Date: 2020
    detail.hit.zdb_id: 2040198-X
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  • 9
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    Online Resource
    Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species
    MDPI AG ; 2022
    In:  Agronomy Vol. 12, No. 2 ( 2022-02-06), p. 412-
    Details
    In: Agronomy, MDPI AG, Vol. 12, No. 2 ( 2022-02-06), p. 412-
    Abstract: Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196 accessions could be grouped into either three (Q) or eight (q) sub-populations. Phylogenetic analysis indicated that most accessions from each species merged. The species S. barberi and S. sinense formed one group. The species S. robustum, S. barberi, S. spontaneum, S. edule, and sugarcane hybrids merged into the second group. The S. officinarum accessions formed the third group located between the other two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four alleles each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five alleles for S. robustum. and three alleles for Saccharum spp. hybrids. These species-specific or species-associated SSR alleles will have a wide application value in sugarcane breeding and species identification. The overall results provide useful information for future genetic study of the Saccharum genus and efficient utilization of sugarcane germplasm resources in sugarcane breeding.
    Type of Medium: Online Resource
    ISSN: 2073-4395
    URL: Article
    DOI: 10.3390/agronomy12020412
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2607043-1
    SSG: 23
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  • 10
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    Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm
    Oxford University Press (OUP) ; 2022
    In:  Horticulture Research Vol. 9 ( 2022-01-05)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 9 ( 2022-01-05)
    Abstract: White rust, caused by Albugo occidentalis, is one of the major yield-limiting diseases of spinach (Spinacia oleracea) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. of Agriculture) germplasm accessions was phenotyped for white rust resistance under field conditions and GWAS was performed using 13 235 whole-genome resequencing (WGR) generated SNPs. Nine SNPs, chr2_53 049 132, chr3_58 479 501, chr3_95 114 909, chr4_9 176 069, chr4_17 807 168, chr4_83 938 338, chr4_87 601 768, chr6_1 877 096, and chr6_31 287 118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson’s correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. The results indicated that a 2- to 10-fold difference in the various GP models had similar, although not identical, averaged r values in each SNP set; using GWAS-derived significant SNP markers would increase PA with a high r-value up to 0.84. The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhac069
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2781828-7
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