Construction of high density genetic map and QTL mapping in sorghum × sudangrass

Euphytica ◽  
2021 ◽  
Vol 217 (8) ◽  
Author(s):  
Peng Jin ◽  
Lihua Wang ◽  
Wenjie Zhao ◽  
Jian Zheng ◽  
Yi-Hong Wang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density ◽  
Sorghum Sudangrass

QTL Mapping for Kernel Related Traits Based on a High-Density Genetic Map

2015 ◽  
Vol 41 (10) ◽  
pp. 1510 ◽  
Author(s):  
Wei-Wei QIN ◽  
Yong-Xiang LI ◽  
Chun-Hui LI ◽  
Lin CHEN ◽  
Xun WU ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

scholarly journals Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zemao Yang ◽  
Youxin Yang ◽  
Zhigang Dai ◽  
Dongwei Xie ◽  
Qing Tang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Qtl Mapping ◽  
Genetic Map ◽  
Quantitative Trait ◽  
High Density ◽  
Genetic Maps ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Qtls Mapping

Abstract Background Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. Results We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. Conclusions We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar

Planta ◽  
2018 ◽  
Vol 248 (5) ◽  
pp. 1173-1185 ◽  
Author(s):  
Wenxiu Xia ◽  
Zheng’ang Xiao ◽  
Pei Cao ◽  
Yan Zhang ◽  
Kebing Du ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
Leaf Shape ◽  
High Density

scholarly journals High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill

2019 ◽  
Vol 10 ◽  
Author(s):  
Zhongtang Wang ◽  
Zhong Zhang ◽  
Haixia Tang ◽  
Qiong Zhang ◽  
Guangfang Zhou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density ◽  
Map Construction ◽  
Ziziphus Jujuba

scholarly journals Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
De Novo ◽  
Fruit Size ◽  
Leaf Size ◽  
High Density ◽  
Potential Candidate ◽  
Goji Berry ◽  
High Density Linkage Map

Abstract Background: Goji (Lycium spp., 2n = 24) is a perennial woody plant bearing functional properties. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but fewer studies have attempted on genomic regions corresponding to the fruit traits.Results: In this study, we established high-resolution map using SLAF-seq for de novo SNPs detection, based on 305 F1 offspring derived from L. chinense and L. barbarum. This genetic map contained 3,495 SNP markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents had sequencing depth of 72.43-fold and 60.43-fold, respectively, while 15.23-fold detected for individuals. Phenotype data were obtained for 2 years and included 3rd year data as an average. QTL mapping analysis resulted in 117 QTLs corresponding to all traits, of which 23 QTLs in 2 years and 6 QTLs in 3rd years were detected. 6 promising QTLs, qFW10-3.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1 and qLA10-2.1 were discovered influencing fruit weight, fruit length and leaf size related attributes covering an interval ranged 13.74-76.61 cM on LG10 with peak LOD up to 14.21 and PVE 19.3%. Additionally, 3 QTLs, qFS-1, qFS-2 and qFF-1, targeting fruit sweetness and fruit firmness were also identified in this study. Strikingly, among stable QTLs, qFL10-2.1, was co-localized to qLL10-2.1, qLD10-2.1, qLA10-2.1 and harbored significantly similar markers distribution, while qLL10-2.1 was the major and stable QTL with LOD ranged from 8.71-14.21 and PVE 12.3-19.3%. As LG10 harbored most of the fruit and leaf size related QTLs, we might speculate that it could be a hotspot region regulating fruit size and plant architectures.Conclusions: This report highlighted that the high-density linkage map construction using SLAF-seq is an important means for profound QTL mapping approach. Substantially, we utilized highly saturated genetic map to find out genetic locus targeting fruit and leaf size related attributes under QTL mapping. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry. Moreover, these findings would facilitate to assemble reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals QTL mapping for quality traits using a high-density genetic map of wheat

PLoS ONE ◽  
2020 ◽  
Vol 15 (3) ◽  
pp. e0230601 ◽  
Author(s):  
Ying Guo ◽  
Guizhi Zhang ◽  
Baojin Guo ◽  
Chunyan Qu ◽  
Mingxia Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density ◽  
Quality Traits

Construction of a high density genetic map and QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing

2020 ◽  
Author(s):  
Junchao Liang ◽  
Yanying Ye ◽  
Xiaowen Yan ◽  
Tingxian Yan ◽  
Yueliang Rao ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Qtl Mapping ◽  
Genetic Map ◽  
Phenotypic Variation ◽  
Root Length ◽  
High Density ◽  
Seedling Stage ◽  
Whole Genome ◽  
Major Qtls ◽  
Ril Population

Abstract BackgroundImprovement in sesame (Sesamum indicum L.) drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. So far, only a few studies have been reported to reveal gene/ quantitative trait loci (QTL) controlling drought tolerance in sesame. To identify the genomic regions associated with drought tolerance, we constructed a high-density genetic map using a recombinant inbred line (RIL) population through whole genome re-sequencing (WGRS) technique. QTLs contributing to three seedling traits were identified under both non-stress and water stress conditions.ResultsThree drought tolerance related traits and their relative values (the ratio of value under stress to value under control condition), including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and PEG-induced osmotic conditions at seedling stage in a RIL population derived from cross of Zhushanbai (ZSB) and Jinhuangma (JHM). Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through WGRS strategy. Composite interval mapping analysis was performed for all the traits as well as their relative phenotypic data. A total of 34 QTLs were detected for these traits under both conditions and their relative values, and 13 stable QTLs associated with seven traits were revealed in two independent experiments, explaining on average, 4.95-16.26% of phenotypic variation for each QTL. Four of them contributed more than 10% of phenotypic variation. One region on chromosome 12 contained two major QTLs related to RL under osmotic condition and relative RL. Seven candidate genes underlying major QTLs for drought tolerance were identified according to gene descriptions and variations between parents.ConclusionThe current study reports the first QTL mapping of drought tolerance related traits through a RIL population and first QTL detection of root related trait (root length) in sesame. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

Sign in / Sign up

Export Citation Format

Share Document