Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58–25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

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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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Construction of a High Density Genetic Map and QTL Mapping of PEG-Induced Drought Tolerance at Seedling Stage in Sesame Using Whole Genome Re-Sequencing

10.21203/rs.3.rs-50720/v1 ◽

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 ◽

Phenotypic Data ◽

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, very 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 three traits under both conditions and their relative values, and 13 stable QTLs associated with seven traits could be 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. Root length related QTLs were first identified in sesame. One region on chromosome 12 contained two major QTLs related to RL under osmotic condition and relative RL. 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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Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population

10.1101/076745 ◽

2016 ◽

Author(s):

RJ Cody Markelz ◽

Michael F Covington ◽

Marcus T Brock ◽

Upendra K Devisetty ◽

Daniel J Kliebenstein ◽

...

Keyword(s):

Genetic Map ◽

Brassica Rapa ◽

Mapping Population ◽

High Density ◽

Rna Seq ◽

Model Species ◽

Map Construction ◽

Genomic Scaffold ◽

Genome Annotations ◽

Genomic Locations

AbstractBrassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here we describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population derived from field collected RNA-seq data. This high-density genotype data enables the detection and correction of putative genome mis-assemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated Brassica rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in finetuning genome annotations.

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Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.043000 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2259-2270 ◽

Cited By ~ 10

Author(s):

R J Cody Markelz ◽

Michael F Covington ◽

Marcus T Brock ◽

Upendra K Devisetty ◽

Daniel J Kliebenstein ◽

...

Keyword(s):

Genetic Map ◽

Brassica Rapa ◽

Mapping Population ◽

High Density ◽

Fine Tuning ◽

Rna Seq ◽

Map Construction ◽

Genomic Scaffold ◽

Genome Annotations ◽

Genomic Locations

Abstract Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1–8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.

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Construction of a High-Density Genetic Map via Genome Resequencing and QTL Detection for Key Fiber Traits in Asiatic Cotton

10.21203/rs.3.rs-53461/v1 ◽

2020 ◽

Author(s):

Yaohua Li ◽

Tong Mo ◽

Lingfang Ran ◽

Jianyan Zeng ◽

Chuannan Wang ◽

...

Keyword(s):

Genetic Map ◽

High Density ◽

Phenotypic Variance ◽

Whole Genome ◽

Qtl Detection ◽

Genome Resequencing ◽

Asiatic Cotton ◽

Ril Population ◽

Fiber Traits ◽

Whole Genome Resequencing

Abstract Background: Asiatic cotton (Gossypium arboreum, genome A2) is one of diploid cotton species producing spinnable fibers. However, few studies on the genetic mechanism of key fiber traits of Asiatic cotton have been reported. Sequencing technology advancement and the release of Asiatic cotton genome made it possible to construct a high-density SNP genetic map and further untapped QTL detection.Results: The Asiatic cotton cultivars SXY No.1 and CSLZ were crossed to develop a recombinant inbred line (RIL) population with 189 lines. Whole genome resequencing technology was employed to construct a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. Based on fiber quality and yield component trait data from three environments, a total of 177 QTL were identified for 8 key fiber traits explaining 5.0-37.4% of the phenotypic variance. Besides, 48 stable QTL, including 15 for upper quartile length (UQL), 18 for fiber fineness (FF), 1 for immature fiber content (IFC), 4 for fiber neps count (FNC), 3 for lint percentage (LP), 7 for seed index (SI), were detected in more than one environment.Conclusions: Using a RIL population and whole genome resequencing strategy, this study presented a high-density genetic map of G. arboreum and identified 48 stable QTL for 6 key fiber traits (UQL, FF, IFC, FNC, LP, SI). Our work laid solid foundation for subsequent fine mapping of QTL for key fiber traits and cloning of controlling genes.

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Construction of ddRADseq-Based High-Density Genetic Map and Identification of Quantitative Trait Loci for Trans-resveratrol Content in Peanut Seeds

Frontiers in Plant Science ◽

10.3389/fpls.2021.644402 ◽

2021 ◽

Vol 12 ◽

Author(s):

Huaiyong Luo ◽

Jianbin Guo ◽

Bolun Yu ◽

Weigang Chen ◽

Huan Zhang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Genetic Map ◽

Quantitative Trait ◽

High Performance ◽

Interval Mapping ◽

Hplc Method ◽

High Density ◽

Nucleotide Polymorphisms ◽

Ril Population ◽

Trait Loci

Resveratrol (trans-3,4′,5-trihydroxystilbene) is a natural stilbene phytoalexin which is also found to be good for human health. Cultivated peanut (Arachis hypogaea L.), a worldwide important legume crop, is one of the few sources of human's dietary intake of resveratrol. Although the variations of resveratrol contents among peanut varieties were observed, the variations across environments and its underlying genetic basis were poorly investigated. In this study, the resveratrol content in seeds of a recombination inbred line (RIL) population (Zhonghua 6 × Xuhua 13, 186 progenies) were quantified by high performance liquid chromatography (HPLC) method across four environments. Genotypes, environments and genotype × environment interactions significantly influenced the resveratrol contents in the RIL population. A total of 8,114 high-quality single nucleotide polymorphisms (SNPs) were identified based on double-digest restriction-site-associated DNA sequencing (ddRADseq) reads. These SNPs were clustered into bins using a reference-based method, which facilitated the construction of high-density genetic map (2,183 loci with a total length of 2,063.55 cM) and the discovery of several chromosome translocations. Through composite interval mapping (CIM), nine additive quantitative trait loci (QTL) for resveratrol contents were identified on chromosomes A01, A07, A08, B04, B05, B06, B07, and B10 with 5.07–8.19% phenotypic variations explained (PVE). Putative genes within their confidential intervals might play roles in diverse primary and secondary metabolic processes. These results laid a foundation for the further genetic dissection of resveratrol content as well as the breeding and production of high-resveratrol peanuts.

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Grain Protein Content QTLs Identified in a Durum × Wild Emmer Wheat Mapping Population Tested in Five Environments

10.1101/601773 ◽

2019 ◽

Cited By ~ 2

Author(s):

Andrii Fatiukha ◽

Itamar Lupo ◽

Gabriel Lidzbarsky ◽

Valentina Klymiuk ◽

Abraham B. Korol ◽

...

Keyword(s):

Protein Content ◽

Genetic Map ◽

Grain Protein Content ◽

High Density ◽

Wild Emmer Wheat ◽

Emmer Wheat ◽

Wild Emmer ◽

Grain Protein ◽

Genetic Dissection ◽

Ril Population

AbstractWild emmer wheat (Triticum turgidumssp.dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore, possess a great potential for improvement of cultivated wheat nutritional value. A recombinant inbred line (RIL) population derived from a cross betweenT. durumvar. Svevo and WEW acc. Y12-3 was used for construction of a high-density genetic map and genetic dissection of GPC. Genotyping of 208 F6RILs with 15K wheat SNP array yielded 4,166 polymorphic SNP markers, of which 1,510 were designated as skeleton markers. A total map length of 2,169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs with LOD score range of 2.7-35.9, and PEV of 2.6-26.6% were identified under five environments. Major QTLs with favorable alleles from WEW were identified on chromosomes 4BS, 5AS, 6BS and 7BL. The QTL region on 6BS coincided with the physical position of the previously cloned QTL,Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum×WEW RIL population led to the identification of four common and two homoeologous QTLs. Exploration of the large genetic variation within WEW accessions is a precondition for discovery of exotic beneficial alleles, as we have demonstrated here, by the identification of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.Key messageGenetic dissection of GPC in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 QTLs, with favorable WEW allele for 11 QTLs.

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