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

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.

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Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number

Frontiers in Plant Science ◽

10.3389/fpls.2020.600788 ◽

2020 ◽

Vol 11 ◽

Author(s):

Qiao Li ◽

Zhifen Pan ◽

Yuan Gao ◽

Tao Li ◽

Junjun Liang ◽

...

Keyword(s):

Genetic Map ◽

Quantitative Trait ◽

Recombinant Inbred Lines ◽

High Density ◽

Genetic Maps ◽

Phenotypic Variance ◽

Quality Traits ◽

Rna Seq ◽

Falling Number ◽

7S Globulin

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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High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

Phytopathology ◽

10.1094/phyto-12-19-0480-r ◽

2021 ◽

pp. PHYTO-12-19-048

Author(s):

Kai Su ◽

Yinshan Guo ◽

Weihao Zhong ◽

Hong Lin ◽

Zhendong Liu ◽

...

Keyword(s):

Qtl Mapping ◽

Dna Sequencing ◽

Quantitative Trait ◽

Restriction Site ◽

Genetic Distances ◽

Snp Markers ◽

High Density ◽

White Rot ◽

Phenotypic Variance ◽

Trait Locus

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca ‘Zhuosexiang’) and white rot-susceptible cultivar (V. vinifera ‘Victoria’). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

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A Novel Stable QTL in Chromosome A04 for Salt Tolerance at the Seed Germination Stage of Upland Cotton via a Resequencing-Based High-Density Genetic Map

10.21203/rs.3.rs-285949/v1 ◽

2021 ◽

Author(s):

Qishen Gu ◽

Huifeng Ke ◽

Chenchen Liu ◽

Xing Lv ◽

Zhengwen Sun ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Genetic Map ◽

Germination Rate ◽

High Density ◽

Virus Induced Gene Silencing ◽

Stable Quantitative Trait Locus ◽

Trait Locus ◽

Functional Analyses

Abstract Key message Two candidate genes GhGASA1 and GhADC2 playing negative roles by modulating the GA and PA signaling pathway, respectively, were identified in a major QTL for germination under salt stress.The successful transition of a seed into a seedling is the prerequisite for plant propagation and crop yield. Germination is a vulnerable stage in a plant’s life cycle which is strongly affected by environmental conditions, such as salinity. In this study, we identified a novel stable quantitative trait locus (QTL) qRGR-A04-1 associated with relative germination rate (RGR) after treatment with salt stress based on a high-density genetic map under phytotron and filed conditions, with LOD values of 6.65-16.83 and 6.11-12.63% of phenotypic variations in all five environment tests. Two candidate genes with significantly differential expression between two parents were finally identified through RNA-seq and qRT-PCR analyses. Further functional analyses showed that GhGASA1- and GhADC2-overexpression lines were more sensitive to salt stress than wild-type in Arabidopsis through regulating the transcript levels of gibberellic acid (GA) and polyamine (PA) -related genes implicating in GA and PA biosynthesis with reducing the accumulation of GA and PA under salt stress, respectively. Virus-induced gene silencing analysis showed that TRV:GASA1 and TRV:ADC2 displayed more tolerant to salt stress by increasing the expression of GA-synthesis genes and decreasing the H2O2 content, respectively. Taken together, our results suggested that QTL qRGR-A04-1 and its harbored two genes, GhGASA1 and GhADC2, were promising candidates for salt tolerance improvement in cotton.

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Construction of a high-density genetic map and identification of quantitative trait loci for nitrite tolerance in the Pacific white shrimp (Litopenaeus vannamei)

10.21203/rs.2.18940/v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Digang Zeng ◽

Xiuli Chen ◽

Weilin Zhu ◽

Min Peng ◽

Chunling Yang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Genetic Map ◽

Quantitative Trait ◽

Molecular Mechanisms ◽

Average Distance ◽

Pacific White Shrimp ◽

High Density ◽

White Shrimp ◽

Phenotypic Variance ◽

Trait Loci

Abstract BackgroundNitrite is a major environmental toxin in aquaculture systems disrupting multiple physiological functions in aquatic animals. Although nitrite tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. ResultsIn this study, we constructed a high-density genetic map of L. vannamei with 17,242 single nucleotide polymorphism markers spanning 6,828.06 centimorgans (cM) and an average distance of 0.4 cM between adjacent markers on 44 linkage groups (LGs). Using this genetic map, we identified 2 quantitative trait loci (QTLs) involved in nitrite tolerance on two LGs explaining 8.42–10.31% of the phenotypic variance. We then sequenced the transcriptomes of the most nitrite-tolerant and the most nitrite-sensitive individuals from each of four genetically distinct L. vannamei families and found 2,002, 1,983, 1,954, and 1,867 differentially expressed genes in the four families, respectively. By integrating QTL and transcriptomics analyses, we identified a candidate gene associated with nitrite tolerance. This gene was annotated as solute carrier family 26 member 6 (SLC26A6). RNA interference (RNAi) analysis demonstrated that SLC26A6 was critical for nitrite tolerance in L. vannamei. ConclusionsThe present study increases our understanding of the molecular mechanisms underlying nitrite tolerance in shrimp, and provides a basis for molecular-marker-assisted shrimp breeding.

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Identification of quantitative trait loci associated with salt tolerance during seedling growth in soybean (Glycine max L.)

Australian Journal of Agricultural Research ◽

10.1071/ar08104 ◽

2008 ◽

Vol 59 (12) ◽

pp. 1086 ◽

Cited By ~ 41

Author(s):

Huatao Chen ◽

Shiyou Cui ◽

Sanxiong Fu ◽

Junyi Gai ◽

Deyue Yu

Keyword(s):

Salt Stress ◽

Quantitative Trait Loci ◽

Salt Tolerance ◽

Seedling Growth ◽

Quantitative Trait ◽

Phenotypic Variance ◽

Linkage Groups ◽

Plant Survival ◽

Greenhouse Experiments ◽

Trait Loci

Salt stress is an important factor affecting the growth and development of soybean. The inheritance and expression of traits associated with salt tolerance during the seedling stage are complex. The present study was conducted to identify quantitative trait loci (QTLs) associated with salt tolerance during seedling growth in soybean. Field and greenhouse experiments were conducted to evaluate 184 recombinant inbred lines (RILs) derived from a cross between Kefeng No. 1 and Nannong1138-2 for salt tolerance and QTLs that are associated with salt tolerance. The molecular map of this RIL population, covering 2625.9 cM of the genome, converged into 24 linkage groups and consisted of 221 SSR markers and 1 disease-resistant gene (Rsc-7). QTL mapping was conducted using WinQTLCart. Eight putative QTLs significantly associated with salt tolerance were identified. One QTL was identified both in field and greenhouse experiments. In the field, salt tolerance was assessed (tolerance rating, TR) visually on a 0 (death) to 5 (unaffected by salt stress) scale. Three QTLs were detected on two linkage groups explaining 7.1–19.7% of the total phenotypic variance for salt tolerance. In the greenhouse, plant survival days (PSD) and percentage of plant survival (PPS) under salt stress were measured. Six QTLs were detected on six linkage groups, and explained 7.8–19.2% of total phenotypic variation for salt tolerance. A major QTL was identified between markers Sat_164 and Sat_358 on linkage group G in both the field and greenhouse. This QTL qppsN.1 was identified in the same location as a salt tolerance QTL previously reported in soybean. The detection of new QTLs will provide important information for marker-assisted selection (MAS) and further genetic studies on salt tolerance in soybean.

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

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2015.01510 ◽

2015 ◽

Vol 41 (10) ◽

pp. 1510 ◽

Cited By ~ 1

Author(s):

Wei-Wei QIN ◽

Yong-Xiang LI ◽

Chun-Hui LI ◽

Lin CHEN ◽

Xun WU ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

High Density

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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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