QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map

Abstract Background Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits, an advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3) population was adopted to phenotypic data acquisitions for the target traits across six distinct environments (seasons and soybean growth stages). Moreover, the restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage map of the RIL population was utilized for QTL mapping by carrying out the composite interval mapping (CIM) approach. Results Correlation analyses showed that most traits were correlated with each other under specific chlorophyll assessing method and were regulated both by hereditary and environmental factors. In this study, 78 QTLs for soybean leaf chlorophyll-content traits were identified. Furthermore, 13 major QTLs and five important QTL hotspots were classified and highlighted from the detected QTLs. Finally, Glyma01g15506, Glyma02g08910, Glyma02g11110, Glyma07g15960, Glyma15g19670 and Glyma15g19810 were predicted from the genetic intervals of the major QTLs and important QTL hotspots. Conclusions The detected QTLs and candidate genes may facilitate to gain a better understanding of the hereditary basis of soybean leaf chlorophyll-content traits and may be valuable to pave the way for the marker-assisted selection (MAS) breeding of the target traits.

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Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

Heredity ◽

10.1038/s41437-019-0238-7 ◽

2019 ◽

Vol 123 (5) ◽

pp. 579-592 ◽

Cited By ~ 10

Author(s):

Jian-Fang Zuo ◽

Yuan Niu ◽

Peng Cheng ◽

Jian-Ying Feng ◽

Shi-Feng Han ◽

...

Keyword(s):

Glycine Max ◽

Qtl Mapping ◽

Linkage Map ◽

Segregation Distortion ◽

High Density ◽

Map Construction ◽

Glycine Max L ◽

Marker Segregation Distortion ◽

High Density Linkage Map

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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

10.21203/rs.3.rs-50720/v2 ◽

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.

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

International Journal of Molecular Sciences ◽

10.3390/ijms22115723 ◽

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.

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The applicability of empirical vegetation indices for determining leaf chlorophyll content over different leaf and canopy structures

Ecological Complexity ◽

10.1016/j.ecocom.2013.11.005 ◽

2014 ◽

Vol 17 ◽

pp. 119-130 ◽

Cited By ~ 68

Author(s):

H. Croft ◽

J.M. Chen ◽

Y. Zhang

Keyword(s):

Chlorophyll Content ◽

Vegetation Indices ◽

Leaf Chlorophyll Content ◽

Leaf Chlorophyll

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RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab130 ◽

2021 ◽

Author(s):

Toshiyuki Sakai ◽

Akira Abe ◽

Motoki Shimizu ◽

Ryohei Terauchi

Keyword(s):

Chlorophyll Content ◽

Recombinant Inbred ◽

Complex Traits ◽

Genetic Architecture ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Gene Interactions ◽

Leaf Chlorophyll Content ◽

Leaf Chlorophyll ◽

Seed Hull

Abstract Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines (RILs) excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.

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