Whole-genome re-sequencing and fine mapping of an orange petal color gene (Bnpc1) in spring Brassica napus L. to a 151-kb region

Yao, Yanmei; Li, Kaixiang; Liu, Haidong; Duncan, Robert; Guo, Shaomin; Xiao, Lü; Du, Dezhi

doi:10.1007/s10681-017-1959-4

Cited by 19 publications

(22 citation statements)

References 52 publications

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“…Geng et al combined specific length amplified fragment sequencing (SLAF-seq) with BSA and identified four candidate genes related to seed weight [25]. Yao et al mapped the orange petal color gene ( Bnpc1 ) in spring B. napus to a 151-kb region via BSA with whole genome re-sequencing (WGR) [26]. Hence, we believed that combining BSA and WGR would be a convenient way to map the genomic regions responsible for the multi-silique trait.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we performed association analysis based on SNP and InDel data using a Euclidean Distance (ED) algorithm to identify the gene underlying the multi-silique trait in rapeseed. Though the SNP-index method is also a classical method for association region identification, and has been employed in many studies [25, 26]. However, it is suitable in the case when four DNA samples are sequenced: two parental plants and two extreme pools from segregated population.…”

Section: Introductionmentioning

confidence: 99%

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Identification of genomic regions associated with multi-silique trait in Brassica napus

Chai

Zhang

et al. 2019

BMC Genomics

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Background Although rapeseed ( Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecular mechanism underlying this beneficial trait remains unclear. Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines (NILs) zws-ms (multi-silique) and zws-217 (single-silique). We used the Euclidean Distance (ED) to identify genomic regions associated with this trait based on both SNPs and InDels. We also conducted transcriptome sequencing to identify differentially expressed genes (DEGs) between zws-ms and zws-217. Results Genetic analysis using the ED algorithm identified three SNP- and two InDel-associated regions for the multi-silique trait. Two highly overlapped parts of the SNP- and InDel-associated regions were identified as important intersecting regions, which are located on chromosomes A09 and C08, respectively, including 2044 genes in 10.20-MB length totally. Transcriptome sequencing revealed 129 DEGs between zws-ms and zws-217 in buds, including 39 DEGs located in the two abovementioned associated regions. We identified candidate genes involved in multi-silique formation in rapeseed based on the results of functional annotation. Conclusions This study identified the genomic regions and candidate genes related to the multi-silique trait in rapeseed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5675-4) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of genomic regions associated with multi-silique trait in Brassica napus

Chai

Zhang

et al. 2019

BMC Genomics

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“…Whole-genome resequencing analysis using BSA could be used to identify candidate intervals, as shown in C. sativus (Lu et al, 2014 ), B. rapa (Wang et al, 2016 ), B. juncea (Zhao et al, 2017 ), and B. napus (Yao et al, 2017 ). Therefore, whole-genome resequencing analysis was conducted for our candidate gene.…”

Section: Resultsmentioning

confidence: 99%

Mapping and Identifying a Candidate Gene (Bnmfs) for Female-Male Sterility through Whole-Genome Resequencing and RNA-Seq in Rapeseed (Brassica napus L.)

Teng

Xiao³

et al. 2017

Front. Plant Sci.

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In oilseed crops, carpel and stamen development play vital roles in pollination and rapeseed yield, but the genetic mechanisms underlying carpel and stamen development remain unclear. Herein, a male- and female-sterile mutant was obtained in offspring of a (Brassica napus cv. Qingyou 14) × (Qingyou 14 × B. rapa landrace Dahuang) cross. Subsequently, F2–F9 populations were generated through selfing of the heterozygote plants among the progeny of each generation. The male- and female-sterility exhibited stable inheritance in successive generations and was controlled by a recessive gene. The mutant kept the same chromosome number (2n = 38) as B. napus parent but showed abnormal meiosis for male and female. One candidate gene for the sterility was identified by simple sequence repeat (SSR) and insertion deletion length polymorphism (InDel) markers in F7–F9 plants, and whole-genome resequencing with F8 pools and RNA sequencing with F9 pools. Whole-genome resequencing found three candidate intervals (35.40–35.68, 35.74–35.75, and 45.34–46.45 Mb) on chromosome C3 in B. napus and candidate region for Bnmfs was narrowed to approximately 1.11-Mb (45.34–46.45 M) by combining SSR and InDel marker analyses with whole-genome resequencing. From transcriptome profiling in 0–2 mm buds, all of the genes in the candidate interval were detected, and only two genes with significant differences (BnaC03g56670D and BnaC03g56870D) were revealed. BnaC03g56870D was a candidate gene that shared homology with the CYP86C4 gene of Arabidopsis thaliana. Quantitative reverse transcription (qRT)-PCR analysis showed that Bnmfs primarily functioned in flower buds. Thus, sequencing and expression analyses provided evidence that BnaC03g56870D was the candidate gene for male and female sterility in the B. napus mutant.

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“…More recently, next-generation sequencing technologies, such as whole-genome re-sequencing (WGR), have been commonly used to identify key loci related to agronomic traits. The sequencing of the B. napus genome [20] facilitated great advances in the identification of key genes related to branch angle [21], seed weight [22], and petal color [23], among others, in rapeseed.…”

Section: Introductionmentioning

confidence: 99%

Rapid Identification of a Genomic Region Conferring Dwarfism in Rapeseed (Brassica napus L.) YA2016-12

Chai

Zhang

et al. 2019

Agronomy

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Plant height is a vital agronomic trait for crops, including oilseed crops such as rapeseed (Brassica napus L.). It affects the crop yield, oil content, and lodging resistance in rapeseed. In this study, we investigated a dwarf trait controlled by a semi-dominant allele in rapeseed. A dwarf line, YA2016-12, was crossed with a tall line, G184-189, and an F2 population was established. Forty of the tallest plants and 40 of the shortest plants from the F2 population were selected and two DNA pools (tall and dwarf) were constructed by the bulked segregant analysis (BSA) method. The two DNA pools and two parental DNAs were then re-sequenced. A sliding window analysis was used to calculate the Δ(SNP-index) and discover an association region on chromosome A03 with a length of 12.4 Mb. Within this region, we found 1225 genes, including 811 genes with non-synonymous or frameshift mutations between YA2016-12 and G184-189. Alignment to known plant height-related orthologs in Arabidopsis thaliana, as well as KEGG pathway and gene ontology annotations, was used to identify nine candidate genes (BnaA03g31770D, BnaA03g37960D, BnaA03g24740D, BnaA03g40550D, BnaA03g26120D, BnaA03g35130D, BnaA03g42350D, BnaA03g25610D, and BnaA03g39850D) involved in gibberellin or cytokinin signaling. Identification of the causal gene for this trait, and of genetic markers linked to favorable alleles, has potential utility for marker-assisted selection to breed rapeseed varieties with improved height.

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Whole-genome re-sequencing and fine mapping of an orange petal color gene (Bnpc1) in spring Brassica napus L. to a 151-kb region

Cited by 19 publications

References 52 publications

Identification of genomic regions associated with multi-silique trait in Brassica napus

Identification of genomic regions associated with multi-silique trait in Brassica napus

Mapping and Identifying a Candidate Gene (Bnmfs) for Female-Male Sterility through Whole-Genome Resequencing and RNA-Seq in Rapeseed (Brassica napus L.)

Rapid Identification of a Genomic Region Conferring Dwarfism in Rapeseed (Brassica napus L.) YA2016-12

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