Dataset Information

QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie.

ABSTRACT: Ramie fiber extracted from ramie stem bark (RSB) is a highly important natural fiber, and therefore, RSB is an economically important plant organ. The genetic basis of RSB traits is poorly understood. In the present study, fiber yield and three RSB traits (bark thickness, bark weight, and fiber output ratio) were subject to quantitative trait locus (QTL) analysis using an F₂ agamous line population derived from two ramie varieties (Qingdaye and Zhongzhu 1). A total of 4338 high-quality single nucleotide polymorphisms were identified using the genotyping-by-sequencing technique and were subsequently used to construct a high-density genetic map spanning 1942.9 cM. Thereafter, QTL analysis identified five, two, four, and four QTLs for bark thickness, bark weight, fiber output ratio, and fiber yield, respectively. A 5.1 cM region that corresponded to a QTL for bark thickness (qBT4a) contained 106 candidate genes, and the Zhongzhu 1 allele of one of the genes, a putative MYB gene (evm.

Model

scaffold7373.133_D1), included a 760-bp insertion that caused premature termination, thereby producing a protein that lacked part of the MYB domain. Because MYB transcription factors play central roles in regulating the development of secondary cellular walls and fiber biosynthesis, we propose evm.

Model

scaffold7373.133_D1 as a likely candidate gene for qBT4a.

SUBMITTER: Liu C

PROVIDER: S-EPMC5647422 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie.

Liu Chan C Zhu Siyuan S Tang Shouwei S Wang Hongwu H Zheng Xia X Chen Xiaorong X Dai Qiuzhong Q Liu Touming T

Scientific reports 20171018 1

Ramie fiber extracted from ramie stem bark (RSB) is a highly important natural fiber, and therefore, RSB is an economically important plant organ. The genetic basis of RSB traits is poorly understood. In the present study, fiber yield and three RSB traits (bark thickness, bark weight, and fiber output ratio) were subject to quantitative trait locus (QTL) analysis using an F<sub>2</sub> agamous line population derived from two ramie varieties (Qingdaye and Zhongzhu 1). A total of 4338 high-qualit ...[more]

PMID: 29044147

Similar Datasets

Project description:Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main quantitative trait loci (QTLs) that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map QTLs for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as recombination-rich areas in all chromosomes except chromosome 1B. Both the genetic map and the physical map showed a significant correlation, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43 cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11 mm. A total of 43 QTLs were identified, including eight QTLs for plant height (PH), 11 QTLs for thousand grain weight (TGW), 15 QTLs for grain length (GL), and nine QTLs for grain width (GW), which explained 1.36-33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci (Qph.nwafu-4B and Qph.nwafu-4D) that determined plant height. The explanation rates of phenotypic variation were 7.39-12.26% and 20.11-27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43-6.85% for phenotypic variation. Two co-segregating KASP markers were developed, and the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB, respectively. Qph.nwafu-4B, controlling plant height, and Qtgw.nwafu-4B, controlling TGW, had an obvious linkage relationship, with a distance of 7-8 cM. Breeding is based on molecular markers that control plant height and thousand-grain weight by selecting strains with low plant height and large grain weight. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43-6.85%. Three loci that affected grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2, and Qgl.nwafu-6B, illustrating the explanation rates of phenotypic variation as 6.72-9.59%, 5.62-7.75%, and 6.68-10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.

Project description:BackgroundFlavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.ResultsA total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.ConclusionsTo our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.

Project description:BACKGROUND:Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. RESULTS:Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. CONCLUSIONS:The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.

Dataset Information

QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie.

Model

Model

Publications

QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets