scholarly journals QTL Mapping for Leaf Area of Tea Plants (Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanlin An ◽  
Linbo Chen ◽  
Lingling Tao ◽  
Shengrui Liu ◽  
Chaoling Wei
Keyword(s):  
Qtl Mapping ◽  
Leaf Area ◽  
Genetic Map ◽  
Tea Plant ◽  
Whole Genome ◽  
Genome Resequencing ◽  
High Quality ◽  
F1 Hybrid ◽  
Small Leaf ◽  
Whole Genome Resequencing

High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on “Jinxuan,” “Yuncha 1” and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.

scholarly journals High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

2018 ◽  
Vol 16 (11) ◽  
pp. 1954-1967 ◽  
Author(s):  
Gaurav Agarwal ◽  
Josh Clevenger ◽  
Manish K. Pandey ◽  
Hui Wang ◽  
Yaduru Shasidhar ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Candidate Gene ◽  
Genetic Map ◽  
Fine Mapping ◽  
Gene Discovery ◽  
High Density ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals QTL mapping of quality traits in peanut using whole-genome resequencing

2021 ◽  
Author(s):  
Ziqi Sun ◽  
Feiyan Qi ◽  
Hua Liu ◽  
Li Qin ◽  
Jing Xu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Whole Genome ◽  
Quality Traits ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon (Citrullus Lanatus L.) Based on Whole-Genome Resequencing

2018 ◽  
Vol 19 (10) ◽  
pp. 3268 ◽  
Author(s):  
Bingbing Li ◽  
Xuqiang Lu ◽  
Junling Dou ◽  
Ali Aslam ◽  
Lei Gao ◽  
...  
Keyword(s):  
Genetic Map ◽  
Citrullus Lanatus ◽  
Snp Markers ◽  
High Density ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Parental Lines ◽  
Whole Genome Resequencing

Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.

Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing

2014 ◽  
Vol 128 (2) ◽  
pp. 259-272 ◽  
Author(s):  
Jeong-Hwan Mun ◽  
Hee Chung ◽  
Won-Hyong Chung ◽  
Mijin Oh ◽  
Young-Min Jeong ◽  
...  
Keyword(s):  
Genetic Map ◽  
Raphanus Sativus ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

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

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.

scholarly journals Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

2020 ◽  
Vol 21 (3) ◽  
pp. 797 ◽  
Author(s):  
Jianfu Jiang ◽  
Xiucai Fan ◽  
Ying Zhang ◽  
Xiaoping Tang ◽  
Xiaomei Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
High Density ◽  
Pcr Analysis ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Phenotypic Data ◽  
Table Grapes ◽  
Whole Genome Resequencing

Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.

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