scholarly journals Map-based cloning and promoter variation analysis of the lobed leaf gene BoLMI1a in ornamental kale (Brassica oleracea L. var. acephala)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Zhang ◽  
Wendi Chen ◽  
Xing Li ◽  
Wenjing Ren ◽  
Li Chen ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Promoter Region ◽  
Leaf Shape ◽  
Dominant Gene ◽  
Orthologous Gene ◽  
Snp Markers ◽  
Leaf Trait ◽  
Shape Formation ◽  
Ornamental Kale ◽  
Lobed Leaf

Abstract Background Leaf shape is an important agronomic trait in ornamental kale (Brassica oleracea L. var. acephala). Although some leaf shape-related genes have been reported in ornamental kale, the detailed mechanism underlying leaf shape formation is still unclear. Here, we report a lobed-leaf trait in ornamental kale, aiming to analyze its inheritance and identify the strong candidate gene. Results Genetic analysis of F2 and BC1 populations demonstrate that the lobed-leaf trait in ornamental kale is controlled by a single dominant gene, termed BoLl-1 (Brassica oleracea lobed-leaf). By performing whole-genome resequencing and linkage analyses, the BoLl-1 gene was finely mapped to a 127-kb interval on chromosome C09 flanked by SNP markers SL4 and SL6, with genetic distances of 0.6 cM and 0.6 cM, respectively. Based on annotations of the genes within this interval, Bo9g181710, an orthologous gene of LATE MERISTEM IDENTITY 1 (LMI1) in Arabidopsis, was predicted as the candidate for BoLl-1, and was renamed BoLMI1a. The expression level of BoLMI1a in lobed-leaf parent 18Q2513 was significantly higher compared with unlobed-leaf parent 18Q2515. Sequence analysis of the parental alleles revealed no sequence variations in the coding sequence of BoLMI1a, whereas a 1737-bp deletion, a 92-bp insertion and an SNP were identified within the BoLMI1a promoter region of parent 18Q2513. Verification analyses with BoLMI1a-specific markers corresponding to the promoter variations revealed that the variations were present only in the lobed-leaf ornamental kale inbred lines. Conclusions This study identified a lobed-leaf gene BoLMI1a, which was fine-mapped to a 127-kb fragment. Three variations were identified in the promoter region of BoLMI1a. The transcription level of BoLMI1a between the two parents exhibited great difference, providing new insight into the molecular mechanism underlying leaf shape formation in ornamental kale.

scholarly journals Promoter Variations Strongly Enhance the Transcription Level of the BoLMI1 Gene, Causing Lobed Leaves in Ornamental Kale (Brassica Oleracea L. Var. Acephala)

2021 ◽  
Author(s):  
Bin Zhang ◽  
Wendi Chen ◽  
Xing Li ◽  
Wenjing Ren ◽  
Li Chen ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Shape Change ◽  
Leaf Shape ◽  
Dominant Gene ◽  
Snp Markers ◽  
Transcription Level ◽  
Leaf Trait ◽  
Shape Formation ◽  
Ornamental Kale ◽  
Lobed Leaf

Abstract Background: Leaf shape is an important agronomic trait in ornamental kale (Brassica oleracea L. var. acephala). Although some leaf shape-related genes have been reported in ornamental kale, the detailed mechanism underlying leaf shape formation is still unclear. Here, we report a lobed-leaf trait in ornamental kale, aiming to analyze its inheritance and identify the strong candidate gene.Results: Genetic analysis of F2 and BC1 populations demonstrate that the lobed-leaf trait in ornamental kale is controlled by a single dominant gene, termed BoLl-1. By performing whole-genome resequencing and linkage analyses, the BoLl-1 gene was finely mapped to a 127-kb interval on chromosome C09 flanked by SNP markers SL4 and SL6, with genetic distances of 0.6 cM and 0.6 cM, respectively. Based on annotations of the genes within this interval, Bo9g181710, an orthologous gene of LATE MERISTEM IDENTITY 1 (LMI1) in Arabidopsis, was predicted as the candidate for BoLl-1, and was renamed BoLMI1. The expression level of BoLMI1 in lobed-leaf parent 18Q2513 was significantly higher compared with unlobed-leaf parent 18Q2515. Sequence analysis of the parental alleles revealed no sequence variations in the coding sequence of BoLMI1, whereas a 1737-bp deletion, a 92-bp insertion and an SNP were identified within the BoLMI1 promoter region of parent 18Q2513. Verification analyses with BoLMI1-specific markers corresponding to the promoter variations revealed that the variations were present only in the lobed-leaf ornamental kale inbred lines.Conclusions: This study demonstrated that promoter variations strongly enhance the transcription level of BoLMI1 and cause the leaf shape change from unlobed to lobed, providing new insight into the molecular mechanism underlying leaf shape formation in ornamental kale.

scholarly journals Fine Mapping and Identification of the Lobed-Leaf Gene in Radish (Raphanus Sativus L.)

2021 ◽  
Author(s):  
xuewei li ◽  
Chaocheng Guo ◽  
Yao Song ◽  
Xiaokang Zhang ◽  
Qiufang Xiong ◽  
...  
Keyword(s):  
Leucine Zipper ◽  
Bulked Segregant Analysis ◽  
Leaf Shape ◽  
Nuclear Gene ◽  
Genotyping By Sequencing ◽  
Orthologous Gene ◽  
Genomic Region ◽  
Factors Affecting ◽  
Leaf Trait ◽  
Lobed Leaf

Abstract Leaf shape is one of the important factors affecting the yield and quality of radish (Raphanus sativus L.). In this study, an F2 population obtained from the cross of the lobed-leaf cultivar J4 with the serrated-leaf cultivar WA was used for genetic analysis and gene mapping of the lobed-leaf trait. The lobed-leaf trait is controlled by a single dominant nuclear gene, and dominant over the serrated-leaf trait. Through bulked segregant analysis (BSA) and genotyping by sequencing (GBS), the lobed-leaf gene was initially mapped to the genomic region from 0.66 Mb to 8.19 Mb on chromosome R7. By using nine insertion/deletion (INDEL) markers, the gene was further narrowed down to a 1.53 Mb region. The comparative analysis of the collinear region between Raphanus sativus and Brassica napus identified Rs390250, an HD-Zip I transcription factor as the most probable candidate gene. Phylogenetic analysis supported that Rs390250 is an RCO (REDUCED COMPLEXITY) orthologous gene, and the single nucleotide variation (C425T) of Rs390250 which caused an amino acid substitution from serine (S) to lysine (L) in conserved leucine zipper domain, may destroy its DNA-binding function and be supposed to response for the morphological variation.

Fine-mapping of a gene for the lobed leaf, BoLl, in ornamental kale (Brassica oleracea L. var. acephala)

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Jie Ren ◽  
Zhiyong Liu ◽  
Jiangtao Du ◽  
Wei Fu ◽  
Ailin Hou ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Fine Mapping ◽  
Ornamental Kale ◽  
Lobed Leaf ◽  
Brassica Oleracea L

Mapping ofRe, a gene conferring the red leaf trait in ornamental kale (Brassica oleraceaL. var.acephala)

2015 ◽  
Vol 134 (4) ◽  
pp. 494-500 ◽  
Author(s):  
Jie Ren ◽  
Zhiyong Liu ◽  
Ruiqing Niu ◽  
Hui Feng
Keyword(s):  
Leaf Trait ◽  
Ornamental Kale

scholarly journals Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Xiao-ping Liu ◽  
Bao-zhen Gao ◽  
Feng-qing Han ◽  
Zhi-yuan Fang ◽  
Li-mei Yang ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Fine Mapping ◽  
Ornamental Kale ◽  
Brassica Oleracea L ◽  
Purple Leaf

scholarly journals Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

2016 ◽  
Vol 114 (1) ◽  
pp. E57-E66 ◽  
Author(s):  
Ryan J. Andres ◽  
Viktoriya Coneva ◽  
Margaret H. Frank ◽  
John R. Tuttle ◽  
Luis Fernando Samayoa ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Leaf Shape ◽  
Primary Source ◽  
Tetraploid Cotton ◽  
Virus Induced Gene Silencing ◽  
Unique Role ◽  
Leaf Formation ◽  
Elevated Expression ◽  
Transcriptomic Signature ◽  
Lobed Leaf

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.

scholarly journals SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 925 ◽  
Author(s):  
Anna E. Palmé ◽  
Jenny Hagenblad ◽  
Svein Øivind Solberg ◽  
Karolina Aloisi ◽  
Anna Artemyeva
Keyword(s):  
Genetic Resources ◽  
Brassica Oleracea ◽  
Morphological Traits ◽  
Single Nucleotide Polymorphism Array ◽  
Plant Genetic Resources ◽  
Snp Markers ◽  
Single Nucleotide ◽  
International Treaty ◽  
White Cabbage ◽  
Passport Data

Around the world, there are more than 1500 genebanks storing plant genetic resources to be used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for future Brassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.

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