Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on 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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A high density genetic map by whole-genome resequencing for QTL fine-mapping and dissecting candidate genes for growth or sex traits in the pearl oyster (Pinctada fucata martensii)

Aquaculture ◽

10.1016/j.aquaculture.2019.734839 ◽

2020 ◽

Vol 519 ◽

pp. 734839 ◽

Cited By ~ 2

Author(s):

Huiru Liu ◽

Hua Zhang ◽

Xiaolan Pan ◽

Meng Xu ◽

Jing Huang ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Map ◽

Fine Mapping ◽

Pearl Oyster ◽

High Density ◽

Pinctada Fucata ◽

Whole Genome ◽

Genome Resequencing ◽

Qtl Fine Mapping ◽

Whole Genome Resequencing

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

Plant Biotechnology Journal ◽

10.1111/pbi.12930 ◽

2018 ◽

Vol 16 (11) ◽

pp. 1954-1967 ◽

Cited By ~ 29

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

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

International Journal of Molecular Sciences ◽

10.3390/ijms19103268 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3268 ◽

Cited By ~ 7

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.

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

Horticulturae ◽

10.3390/horticulturae7120534 ◽

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.

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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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Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Scientific Reports ◽

10.1038/s41598-021-87445-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Luciano Calderón ◽

Nuria Mauri ◽

Claudio Muñoz ◽

Pablo Carbonell-Bejerano ◽

Laura Bree ◽

...

Keyword(s):

Genetic Diversity ◽

Somatic Mutations ◽

Clonal Propagation ◽

Variant Calling ◽

Vitis Vinifera L ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Genome Resequencing ◽

Diversity Pattern ◽

Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

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QTL Mapping of Quality Related Traits in Peanut Using Whole-Genome Resequencing

10.21203/rs.3.rs-138961/v1 ◽

2021 ◽

Author(s):

Ziqi Sun ◽

Feiyan Qi ◽

Hua Liu ◽

Li Qin ◽

Jing Xu ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Protein Content ◽

Genomic Region ◽

High Density ◽

Whole Genome ◽

Missense Mutations ◽

Genome Resequencing ◽

Phenotypic Effect ◽

Whole Genome Resequencing

Abstract Background: Oil and protein content, as well as fatty acid composition, are important quality traits in peanut. Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars through molecular breeding techniques.Results: Whole-genome resequencing of an RIL population of 318 lines was performed to construct a high-density linkage map and identify QTLs for peanut quality. The map, containing 4561 bin markers, covered a length of 2032.39 cM with an average marker density of 0.45 cM. A total of 109 QTLs for oil content, protein content, and fatty acid compositions were mapped on the 18 peanut chromosomes. The QTL qA05.1 was detected in four different environments and exhibited a major phenotypic effect on the content of oil, proteins, and six fatty acids. The genomic region spanned by qA05.1, corresponding to a physical interval of approximately 1.50 Mb, contains two polymorphic SNPs between two parents that could cause missense mutations. The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents; these sites may be useful in the marker-assisted breeding of peanut varieties with high oil contents.Conclusions: A high-density genetic map with 4561 bin markers was constructed, and a major and pleiotropic QTL located on LG05 was stably detected for oil, protein and fatty acids across four different environments.

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Construction of a High-density Genetic Map and Identification of Candidate Genes for Resistance to Fusarium Wilt based on the Resequencing of Recombinant Inbred Line Population in Gossypium Barbadense

10.21203/rs.3.rs-139530/v1 ◽

2021 ◽

Author(s):

Wanli Han ◽

Jieyin Zhao ◽

Xiaojuan Deng ◽

Aixing Gu ◽

Duolu Li ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Map ◽

Fusarium Wilt ◽

Recombinant Inbred ◽

Gene Annotation ◽

Recombinant Inbred Lines ◽

Fiber Quality ◽

Gossypium Barbadense ◽

High Density ◽

Pcr Analysis

Abstract Background: Resistance to Fusarium wilt (FW) is of great significance for increasing the yield of Gossypium barbadense. Most published genetic studies on G. barbadense focus on yield and fiber quality traits, while there are few reports on resistance to FW. Results: To understand the genetic basis of cotton resistance to FW, this study used 110 recombinant inbred lines (RILs) of G. barbadense obtained from the parental materials Xinhai 14 and 06-146, and Nannong was used to construct a high-density genetic linkage map. The high-density genetic map was based on the resequencing of 933,845 single-nucleotide polymorphism (SNP) markers, and 3627 bins covering 2483.17 cM were finally obtained. The collinearity matched the physical map. A total of 9 QTLs for FW resistance were identified, each QTL explained 4.27-14.92% of the observed phenotypic variation, and qFW-Dt3-1 was identified in at least two environments. According to gene annotation information from multiple databases, promoter homeopathic elements and transcriptome data, 10 candidate genes were screened in a stable QTL interval. qRT-PCR analysis showed that the GOBAR_DD06292 gene was differentially expressed in the roots of the two parents under FW stress and exhibited the same expression trend in the G. barbadense resource materials.Conclusions: These results indicate the importance of the GOBAR_DD06292 gene in FW resistance in G. barbadense and lay a molecular foundation for the analysis of the molecular mechanism of FW in G. barbadense.

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