Identification and fine mapping of a major locus controlling branching in Brassica napus

Li, Bao; Gao, Jinxiang; Chen, Jiao; Wang, Zhixin; Shen, Wenhao; Yi, Bin; Wen, Jing; Ma, Chaozhi; Fu, Tingdong; Tu, Jinxing

doi:10.1007/s00122-019-03506-x

Cited by 25 publications

(17 citation statements)

References 39 publications

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“…GBS has been used for marker discovery, linkage mapping and QTL analysis in a range of crops [12][13][14], including the important oilseed crop Brassica napus. Over 20 high density linkage maps have been generated for B. napus using RNA sequencing [15], the Brassica 60 K genotyping array [16,17] and ddRAD sequencing [18]. Combined with phenotypic data, these linkage maps provide a powerful basis for identification of genes underlying agronomic traits, which can then be introduced into crop germplasm [19,20].…”

Section: Introductionmentioning

confidence: 99%

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

et al. 2020

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Background Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. Results Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. Conclusions These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.

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Section: Introductionmentioning

confidence: 99%

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

et al. 2020

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“…Disrupting the conserved motif of these two genes changed auxin signaling, resulting in plant height changing from tall to dwarf. In the past two decades, a few quantitative trait loci (QTL) and candidate genes for branching-related traits were identified, but none have yet to be functionally validated [ 21 , 22 , 23 , 24 , 25 ]. Hence, our knowledge of the molecular mechanism underlying plant architecture in B. napus remains limited and awaits exploration.…”

Section: Introductionmentioning

confidence: 99%

Combined BSA-Seq Based Mapping and RNA-Seq Profiling Reveal Candidate Genes Associated with Plant Architecture in Brassica napus

Yan

et al. 2022

IJMS

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Plant architecture involves important agronomic traits affecting crop yield, resistance to lodging, and fitness for mechanical harvesting in Brassica napus. Breeding high-yield varieties with plant architecture suitable for mechanical harvesting is the main goal of rapeseed breeders. Here, we report an accession of B. napus (4942C-5), which has a dwarf and compact plant architecture in contrast to cultivated varieties. A BC8 population was constructed by crossing a normal plant architecture line, 8008, with the recurrent parent 4942C-5. To investigate the molecular mechanisms underlying plant architecture, we performed phytohormone profiling, bulk segregant analysis sequencing (BSA-Seq), and RNA sequencing (RNA-Seq) in BC8 plants with contrasting plant architecture. Genetic analysis indicated the plant architecture traits of 4942C-5 were recessive traits controlled by multiple genes. The content of auxin (IAA), gibberellin (GA), and abscisic acid (ABA) differed significantly between plants with contrasting plant architecture in the BC8 population. Based on BSA-Seq analysis, we identified five candidate intervals on chromosome A01, namely those of 0 to 6.33 Mb, 6.45 to 6.48 Mb, 6.51 to 6.53 Mb, 6.77 to 6.79 Mb, and 7 to 7.01 Mb regions. The RNA-Seq analysis revealed a total of 4378 differentially expressed genes (DEGs), of which 2801 were up-regulated and 1577 were down-regulated. There, further analysis showed that genes involved in plant hormone biosynthesis and signal transduction, cell structure, and the phenylpropanoid pathway might play a pivotal role in the morphogenesis of plant architecture. Association analysis of BSA-Seq and RNA-Seq suggested that seven DEGs involved in plant hormone signal transduction and a WUSCHEL-related homeobox (WOX) gene (BnaA01g01910D) might be candidate genes responsible for the dwarf and compact phenotype in 4942C-5. These findings provide a foundation for elucidating the mechanisms underlying rapeseed plant architecture and should contribute to breed new varieties suitable for mechanization.

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“…It was designed based on genomic data of B. napus (AACC, 2 n = 38), the hybrid between B. oleracea and B. rapa [ 40 ]. Since then, several studies have applied this array for analyses in B. napus [ 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 ], among others and B. oleracea [ 18 , 54 , 55 , 56 ], but there have been no published studies focusing on kale that used this array.…”

Section: Introductionmentioning

confidence: 99%

Different Shades of Kale—Approaches to Analyze Kale Variety Interrelations

Kuhnert

Howard

Albach

2022

Genes

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Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.

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Identification and fine mapping of a major locus controlling branching in Brassica napus

Cited by 25 publications

References 39 publications

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

Combined BSA-Seq Based Mapping and RNA-Seq Profiling Reveal Candidate Genes Associated with Plant Architecture in Brassica napus

Different Shades of Kale—Approaches to Analyze Kale Variety Interrelations

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