Identification and validation of a major QTL controlling the presence/absence of leaf lobes in Brassica rapa L.

Wang, Yugang; Liu, Xuejun; Ji, Xiaohong; Zhang, Lei; Liu, Yating; Lv, Xixi; Feng, Hui

doi:10.1007/s10681-015-1403-6

Cited by 20 publications

(14 citation statements)

References 29 publications

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“…NIL development is a useful method for confirming and evaluating the genetic effects of a QTL and provides useful materials for population development during fine mapping of QTLs (Ding et al, 2011 ). This method has been successfully applied for fine mapping of QTLs in most crop species (Benson et al, 2015 ; Jang et al, 2015 ; Wang et al, 2015 ; Zheng et al, 2015 ). In the present study, we developed NILs in a backcrossing program using two parents, Xiushui79 (the receipt parent) and C-bao (the donor parent).…”

Section: Discussionmentioning

confidence: 99%

Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Liu

et al. 2016

Front. Plant Sci.

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Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6, and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9, and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1 encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice.

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Section: Discussionmentioning

confidence: 99%

Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Liu

et al. 2016

Front. Plant Sci.

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“…In B. rapa , the formation of leaf lobes is influenced by QTL on LG A10 30 , 33 . BrLMI1 is located on LG A10 in B. rapa , and a homolog of this gene LOBED-LEAF 1 ( BnLL1 ) is considered responsible for leaf morphology in Brassica napus 34 .…”

Section: Discussionmentioning

confidence: 99%

“…An analysis of leaf morphology of B. rapa showed that the TCP genes are involved in leaf bulge and head formation 25 . In addition, a leaf lobe-related gene has been identified on LG A10 30 , 33 , and a homolog of LATE MERISTEM IDENTITY 1 ( BrLMI1 ) is considered a potential candidate associated with leaf lobe development 34 . Furthermore, next-generation sequencing (NGS) technology enables rapid and high-throughput QTL detection.…”

Section: Introductionmentioning

confidence: 99%

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

et al. 2021

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Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna.

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“…All of the above traits were determined for five plants per line and three leaves per plant. The values of LL, LW, PL and LTL were measured using a ruler as described by Wang et al (2015) [15]. The SAS 9.0 program (SAS Institute, Inc., Cary, NC, USA) was used for distribution analysis.…”

Section: Methodsmentioning

confidence: 99%

“…QTLs have been identified for leaf morphology in Brassica rapa [14, 15], tomato [16], grape [17], oak [18], maize [19], and Arabidopsis [20], suggesting that leaf morphological variation is controlled by multiple genes. QTLs for leaf architecture have also been identified in Brassica species [21–24].…”

Section: Introductionmentioning

confidence: 99%

Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.)

et al. 2017

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Leaf size and shape play important roles in agronomic traits, such as yield, quality and stress responses. Wide variations in leaf morphological traits exist in cultivated varieties of many plant species. By now, the genetics of leaf shape and size have not been characterized in Brassica napus. In this study, a population of 172 recombinant inbred lines (RILs) was used for quantitative trait locus (QTL) analysis of leaf morphology traits. Furthermore, fresh young leaves of extreme lines with more leaf lobes (referred to as ‘A’) and extreme lines with fewer lobes (referred to as ‘B’) selected from the RIL population and leaves of dissected lines (referred to as ‘P’) were used for transcriptional analysis. A total of 31 QTLs for the leaf morphological traits tested in this study were identified on 12 chromosomes, explaining 5.32–39.34% of the phenotypic variation. There were 8, 6, 2, 5, 8, and 2 QTLs for PL (petiole length), PN (lobe number), LW (lamina width), LL (Lamina length), LL/LTL (the lamina size ratio) and LTL (leaf total length), respectively. In addition, 74, 1,166 and 1,272 differentially expressed genes (DEGs) were identified in ‘A vs B’, ‘A vs P’ and ‘B vs P’ comparisons, respectively. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the functions of these DEGs. Gene regulators of leaf shape and size, such as ASYMMETRIC LEAVES 2, gibberellin 20-oxidase 3, genes encoding gibberellin-regulated family protein, genes encoding growth-regulating factor and KNOTTED1-like homeobox were also detected in DEGs. After integrating the QTL mapping and RNA sequencing data, 33 genes, including a gene encoding auxin-responsive GH3 family protein and a gene encoding sphere organelles protein-related gene, were selected as candidates that may control leaf shape. Our findings should be valuable for studies of the genetic control of leaf morphological trait regulation in B. napus.

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Identification and validation of a major QTL controlling the presence/absence of leaf lobes in Brassica rapa L.

Cited by 20 publications

References 29 publications

Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.)

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