Fine mapping and candidate gene analysis of the yellow petal gene ckpc in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by whole-genome resequencing

2019 ◽  
Vol 39 (7) ◽  
Author(s):  
XiaoMei Xu ◽  
Wenlong Luo ◽  
Juxian Guo ◽  
Hancai Chen ◽  
Waheed Akram ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Brassica Oleracea ◽  
Fine Mapping ◽  
Gene Analysis ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Chinese Kale ◽  
Whole Genome Resequencing ◽  
Yellow Petal ◽  
Brassica Oleracea L

scholarly journals High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

2018 ◽  
Vol 16 (11) ◽  
pp. 1954-1967 ◽  
Author(s):  
Gaurav Agarwal ◽  
Josh Clevenger ◽  
Manish K. Pandey ◽  
Hui Wang ◽  
Yaduru Shasidhar ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Candidate Gene ◽  
Genetic Map ◽  
Fine Mapping ◽  
Gene Discovery ◽  
High Density ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Molecular dissection of resistance gene cluster and candidate gene identification of Pl17 and Pl19 in sunflower by whole-genome resequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Guojia Ma ◽  
Qijian Song ◽  
William R. Underwood ◽  
Zhiwei Zhang ◽  
Jason D. Fiedler ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Gene Cluster ◽  
Resistance Gene ◽  
Snp Markers ◽  
Reference Sequence ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Density Mapping ◽  
Family Protein ◽  
Whole Genome Resequencing

Abstract Sunflower (Helianthus annuus L.) production is challenged by different biotic and abiotic stresses, among which downy mildew (DM) is a severe biotic stress that is detrimental to sunflower yield and quality in many sunflower-growing regions worldwide. Resistance against its infestation in sunflower is commonly regulated by single dominant genes. Pl17 and Pl19 are two broad-spectrum DM resistance genes that have been previously mapped to a gene cluster spanning a 3.2 Mb region at the upper end of sunflower chromosome 4. Using a whole-genome resequencing approach combined with a reference sequence-based chromosome walking strategy and high-density mapping populations, we narrowed down Pl17 to a 15-kb region flanked by SNP markers C4_5711524 and SPB0001. A prospective candidate gene HanXRQChr04g0095641 for Pl17 was identified, encoding a typical TNL resistance gene protein. Pl19 was delimited to a 35-kb region and was approximately 1 Mb away from Pl17, flanked by SNP markers C4_6676629 and C4_6711381. The only gene present within the delineated Pl19 locus in the reference genome, HanXRQChr04g0095951, was predicted to encode an RNA methyltransferase family protein. Six and eight SNP markers diagnostic for Pl17 and Pl19, respectively, were identified upon evaluation of 96 diverse sunflower lines, providing a very useful tool for marker-assisted selection in sunflower breeding programs.

scholarly journals Fine Mapping and Whole-Genome Resequencing Identify the Seed Coat Color Gene in Brassica rapa

PLoS ONE ◽  
2016 ◽  
Vol 11 (11) ◽  
pp. e0166464 ◽  
Author(s):  
Yanhua Wang ◽  
Lu Xiao ◽  
Shaomin Guo ◽  
Fengyun An ◽  
Dezhi Du
Keyword(s):  
Brassica Rapa ◽  
Fine Mapping ◽  
Seed Coat ◽  
Coat Color ◽  
Whole Genome ◽  
Seed Coat Color ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Coat Color Gene ◽  
Color Gene

scholarly journals High-Density Mapping and Candidate Gene Analysis of Pl18 and Pl20 in Sunflower by Whole-Genome Resequencing

2020 ◽  
Vol 21 (24) ◽  
pp. 9571
Author(s):  
Guojia Ma ◽  
Qijian Song ◽  
Xuehui Li ◽  
Lili Qi
Keyword(s):  
Candidate Gene ◽  
High Density ◽  
Chromosome 8 ◽  
Reference Sequence ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Putative Gene ◽  
Density Mapping ◽  
New Genes ◽  
Whole Genome Resequencing

Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl18 and Pl20 conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl18 was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl18 was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl20 gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl20, HanXRQChr08g0210051, was identified within the Pl20 interval. SNP markers closely linked to Pl18 and Pl20 were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl18 and four for Pl20 were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.

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