Generation and mapping of SCAR and CAPS markers linked to the seed coat color gene in Brassica napus using a genome-walking technique

Genome ◽  
2007 ◽  
Vol 50 (7) ◽  
pp. 611-618 ◽  
Author(s):  
Shushu Xiao ◽  
Jinsong Xu ◽  
Yuan Li ◽  
Lei Zhang ◽  
Shijun Shi ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Seed Coat ◽  
Coat Color ◽  
Aflp Markers ◽  
Seed Color ◽  
Seed Coat Color ◽  
A Genome ◽  
Reference Map ◽  
Coat Color Gene ◽  
Color Gene

The yellow seed coat trait in No. 2127-17, a resynthesized purely yellow Brassica napus line, is controlled by a single partially dominant gene, Y. A double-haploid population derived from the F1 of No. 2127-17 × ‘ZY821’ was used to map the seed coat color phenotype. A combination of AFLP analysis and bulked segregant analysis identified 18 AFLP markers linked to the seed coat color trait. The 18 AFLP markers were mapped to a chromosomal region of 37.0 cM with an average of 2.0 cM between adjacent markers. Two markers, AFLP-K and AFLP-H, bracketed the Y locus in an interval of 1.0 cM, such that each was 0.5 cM away from the Y locus. Two other markers, AFLP-A and AFLP-B, co-segregated with the seed color gene. For ease of use in breeding programs, these 4 most tightly linked AFLP markers were converted into reliable PCR-based markers. SCAR-K, which was derived from AFLP-K, was assigned to linkage group 9 (N9) of a B. napus reference map consisting of 150 commonly used SSR (simple sequence repeat) markers. Furthermore, 2 SSR markers (Na14-E08 and Na10-B07) linked to SCAR-K on the reference map were reversely mapped to the linkage map constructed in this study, and also showed linkage to the Y locus. These linked markers would be useful for the transfer of the dominant allele Y from No. 2127-17 to elite cultivars using a marker-assisted selection strategy and would accelerate the cloning of the seed coat color gene.

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 Mapping and identification of yellow seed coat color genes in Brassica juncea L.

2020 ◽  
Author(s):  
Zhen Huang ◽  
Yang Wang ◽  
Hong Lu ◽  
Xiang Liu ◽  
Lu Liu ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Brassica Juncea ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Color ◽  
Seed Coat Color ◽  
Flavonoid Pathway ◽  
Yellow Seed ◽  
Color Formation ◽  
Yellow Seed Coat

Abstract BackgroundYellow seed breeding is an effective method to improve the oil content in rapeseed. Yellow seed coat color formation is influenced by various factors, and no clear mechanisms are known. In this study, Bulked segregant RNA-Seq (BSR-Seq) of BC9 population of Wuqi mustard (yellow seed) and Wugong mustard (brown seed) was used to identity the candidate genes controlling the yellow seed color in Brassica juncea L.ResultsYellow seed coat color gene was mapped to chromosome A09, and differentially expressed genes (DEGs) between brown and yellow bulks enriched in the flavonoid pathway. A significant correlation between the expression of BjF3H and BjTT5 and the content of the seed coat color related indexes was identified. Two intron polymorphism (IP) markers linked to the target gene were developed around BjF3H. Therefore, BjF3H was considered as the candidate gene. The BjF3H coding sequences (CDS) of Wuqi mustard and Wugong mustard are 1071-1077bp, encoding protein of 356-358 amino acids. One amino acid change (254, F/V) was identified in the conserved domain. This mutation site was detected in four Brassica rapa (B. rapa) and six Brassica juncea (B. juncea) lines, but not in Brassica napus (B. napus).ConclusionsThe results indicated BjF3H is a candidate gene that related to yellow seed coat color formation in Brassica juncea and provided a comprehensive understanding of the yellow seed coat color mechanism.

Genome-Wide Association Mapping of Seed Coat Color in Brassica napus

2017 ◽  
Vol 65 (26) ◽  
pp. 5229-5237 ◽  
Author(s):  
Jia Wang ◽  
Xiaohua Xian ◽  
Xinfu Xu ◽  
Cunmin Qu ◽  
Kun Lu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Mapping ◽  
Seed Coat ◽  
Coat Color ◽  
Genome Wide Association ◽  
Seed Coat Color ◽  
Genome Wide

QTL Mapping of Seed Coat Color for Yellow Seeded Brassica napus

2006 ◽  
Vol 33 (2) ◽  
pp. 181-187 ◽  
Author(s):  
Lie-Zhao LIU ◽  
Jin-Ling MENG ◽  
Na LIN ◽  
Li CHEN ◽  
Zhang-Lin TANG ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Qtl Mapping ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color

Inheritance of seed coat color genes in Brassica napus (L.) and tagging the genes using SRAP, SCAR and SNP molecular markers

2010 ◽  
Vol 26 (3) ◽  
pp. 439-453 ◽  
Author(s):  
Mukhlesur Rahman ◽  
Genyi Li ◽  
Dana Schroeder ◽  
Peter B. E. McVetty
Keyword(s):  
Molecular Markers ◽  
Brassica Napus ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color ◽  
Brassica Napus L

Inheritance of seed coat color of Ethiopian mustard (Brassica carinata A. Braun)

2010 ◽  
Vol 90 (3) ◽  
pp. 279-281 ◽  
Author(s):  
M Rahman ◽  
M Tahir
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Brassica Carinata ◽  
Seed Coat Color ◽  
Yellow Light ◽  
Ethiopian Mustard ◽  
Light Yellow ◽  
Inheritance Model ◽  
Pure Lines ◽  
Color Gene

The inheritance of seed coat color was investigated in Brassica carinata in F1, F2, F3 and backcross progenies of crosses between brown- and yellow-seeded pure lines. Seed coat color in B. carinata was not influenced by xenia effect. Segregation pattern followed a mono-genic incomplete dominance inheritance model The occurrence of yellow/light yellow-brown seed trait in B. carinata may be due to an interaction between brown seed coat color gene and dominant repressor (Rp) genes. Key words: Brassica carinata, inheritance, seed coat color, dominant repressor

scholarly journals Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 977
Author(s):  
Ai Lin ◽  
Jinqi Ma ◽  
Fei Xu ◽  
Wen Xu ◽  
Huanhuan Jiang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Seed Coat ◽  
Rna Binding ◽  
Developmental Stages ◽  
Coat Color ◽  
Intron Retention ◽  
Seed Color ◽  
Seed Coat Color ◽  
Flavonoid Pathway ◽  
Transcriptional Regulatory

Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.

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