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  • 11
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    DataSheet1.xlsx
    Frontiers Media SA ; 2021
    In:  Frontiers in Genetics Vol. 12 ( 2021-12-8)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 12 ( 2021-12-8)
    Abstract: Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica , and the selective sweeps involved in domestication of cultivated spinach, S. oleracea , from S. turkestanica . A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q 1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q 2 and Q 3. The Q 2 group shared greater genetic identity with the S. oleracea accessions, Q 1, than the Q 3 S. turkestanica group. Likewise, the S. oleracea Q 1 group had a smaller F st (0.008) with the Q 2 group than with the Q 3 group ( F st = 0.012), and a greater gene flow (Nm = 30.13) with the Q 2 group than with the Q 3 group (Nm = 21.83). The Q 2 accessions originated primarily from Uzbekistan while the Q 3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q 2 and Q 3 groups of S. turkestanica . Accessions with admixtures of Q 2 and Q 3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2021.740437
    DOI: 10.3389/fgene.2021.740437.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606823-0
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  • 12
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    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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  • 13
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    Identification of molecular markers for Sw-5 gene of tomato spotted wilt virus resistance
    Science Hub ; 2011
    In:  American Journal of Biotechnology and Molecular Sciences Vol. 1, No. 1 ( 2011-04), p. 8-16
    Details
    In: American Journal of Biotechnology and Molecular Sciences, Science Hub, Vol. 1, No. 1 ( 2011-04), p. 8-16
    Type of Medium: Online Resource
    ISSN: 2159-3701
    URL: Article
    DOI: 10.5251/ajbms.2011.1.1.8.16
    Language: Unknown
    Publisher: Science Hub
    Publication Date: 2011
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  • 14
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    Molecular Markers for Tm-2 Alleles of Tomato Mosaic Virus Resistance in Tomato
    Scientific Research Publishing, Inc. ; 2011
    In:  American Journal of Plant Sciences Vol. 02, No. 02 ( 2011), p. 180-189
    Details
    In: American Journal of Plant Sciences, Scientific Research Publishing, Inc., Vol. 02, No. 02 ( 2011), p. 180-189
    Type of Medium: Online Resource
    ISSN: 2158-2742 , 2158-2750
    URL: Article
    DOI: 10.4236/ajps.2011.22020
    Language: Unknown
    Publisher: Scientific Research Publishing, Inc.
    Publication Date: 2011
    detail.hit.zdb_id: 2635691-0
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  • 15
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    Evaluation of Total Seed Protein Content in Eleven Arkansas Cowpea (〈i〉Vigna unguiculata〈/i〉 (L.) Walp.) Lines
    Scientific Research Publishing, Inc. ; 2016
    In:  American Journal of Plant Sciences Vol. 07, No. 15 ( 2016), p. 2288-2296
    Details
    In: American Journal of Plant Sciences, Scientific Research Publishing, Inc., Vol. 07, No. 15 ( 2016), p. 2288-2296
    Type of Medium: Online Resource
    ISSN: 2158-2742 , 2158-2750
    URL: Article
    DOI: 10.4236/ajps.2016.715201
    Language: Unknown
    Publisher: Scientific Research Publishing, Inc.
    Publication Date: 2016
    detail.hit.zdb_id: 2635691-0
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  • 16
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    Genome-Wide Identification, Classification and Evolutionary Expansion of KNOX Gene Family in Rice (〈i〉Oryza sativa〈/i〉) and 〈i〉Populus〈/i〉 (〈i〉Populustrichocarpa〈/i〉)
    Scientific Research Publishing, Inc. ; 2018
    In:  American Journal of Plant Sciences Vol. 09, No. 06 ( 2018), p. 1071-1092
    Details
    In: American Journal of Plant Sciences, Scientific Research Publishing, Inc., Vol. 09, No. 06 ( 2018), p. 1071-1092
    Type of Medium: Online Resource
    ISSN: 2158-2742 , 2158-2750
    URL: Article
    DOI: 10.4236/ajps.2018.96082
    Language: Unknown
    Publisher: Scientific Research Publishing, Inc.
    Publication Date: 2018
    detail.hit.zdb_id: 2635691-0
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  • 17
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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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  • 18
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    Table_1.xlsx
    Frontiers Media SA ; 2022
    In:  Frontiers in Plant Science Vol. 13 ( 2022-10-6)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 13 ( 2022-10-6)
    Abstract: Spinach ( Spinacia oleracea ) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci ( RPF3 ) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the  RPF3  locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2022.1012923
    DOI: 10.3389/fpls.2022.1012923.s001
    DOI: 10.3389/fpls.2022.1012923.s002
    DOI: 10.3389/fpls.2022.1012923.s003
    DOI: 10.3389/fpls.2022.1012923.s004
    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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  • 19
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    Two Tightly Linked Genes for Soybean Mosaic Virus Resistance in Soybean
    Wiley ; 2017
    In:  Crop Science Vol. 57, No. 4 ( 2017-07), p. 1844-1853
    Details
    In: Crop Science, Wiley, Vol. 57, No. 4 ( 2017-07), p. 1844-1853
    Abstract: Soybean mosaic virus (SMV), a member of the Potyviridae family, is the most common virus negatively affecting yield and seed quality in soybean [ Glycine max (L.) Merr.]. Seven SMV strains, G1 through G7, and three independent SMV resistance genes ( R ‐genes), Rsv1, Rsv3 , and Rsv4 , have been previously identified. The Rsv1 locus contains at least 10 alleles conferring differential plant reactions to SMV strains, and it was mapped at very complex resistance‐gene‐rich region. In this study, two alleles of the Rsv1 locus were analyzed by crossing PI 96983 ( Rsv1 ) and cultivar York ( Rsv1‐y ) soybean to evaluate whether Rsv1 and Rsv1‐y belong to the same or different but closely linked loci. To break possible linkage, 3000 F 2:3 lines were developed and investigated using infections of the SMV‐G1 strain in a greenhouse. The occurrence of segregating and susceptible lines indicated tight linkage between two genes. The recombination frequency (RF) was estimated using the maximum likelihood (ML) formula concluding that Rsv1 and Rsv1‐y are two tightly linked loci located apart with genetic distance of 2.2 cM on chromosome 13. A new symbol of Rsv5 has been assigned for the resistance gene in York to replace the original Rsv1‐y allele assignment. This research provided the first evidence for existence of two R ‐genes on chromosome 13, conferring resistance to different SMV strains. Both loci, Rsv1 and Rsv5 , can be easily transferred into susceptible cultivars in a breeding program to provide broad and durable protection against SMV strains.
    Type of Medium: Online Resource
    ISSN: 0011-183X , 1435-0653
    URL: Article
    DOI: 10.2135/cropsci2016.05.0290
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 1480918-7
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  • 20
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    Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio
    Oxford University Press (OUP) ; 2023
    In:  Horticulture Research Vol. 10, No. 6 ( 2023-06-04)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 10, No. 6 ( 2023-06-04)
    Abstract: Commercial production of spinach (Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance (R) genes. Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P. effusa and were used to study for genetic transmission and mapping analysis in this study. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP (Chr3_1, 221, 009) showing a LOD value of 61.6 in the GLM model in TASSEL, which was within 1.08 Kb from Spo12821, a gene that encodes CC-NBS-LRR plant disease resistance protein. In addition, a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18–1.23 and 1.75–1.76 Mb. This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale. The RPF2 and RPF3 specific SNP markers, plus the resistant genes reported here, could add value to breeding efforts to develop downy mildew resistant cultivars in the future.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhad076
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2781828-7
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