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

Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl18 and Pl20 conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl18 was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl18 was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl20 gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl20, HanXRQChr08g0210051, was identified within the Pl20 interval. SNP markers closely linked to Pl18 and Pl20 were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl18 and four for Pl20 were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.

Download Full-text

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.

Download Full-text

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.

Download Full-text

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.

Download Full-text

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

International Journal of Molecular Sciences ◽

10.3390/ijms21030797 ◽

2020 ◽

Vol 21 (3) ◽

pp. 797 ◽

Cited By ~ 1

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.

Download Full-text

Fine mapping and candidate gene analysis of the yellow petal gene ckpc in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by whole-genome resequencing

Molecular Breeding ◽

10.1007/s11032-019-1011-6 ◽

2019 ◽

Vol 39 (7) ◽

Cited By ~ 3

Author(s):

XiaoMei Xu ◽

Wenlong Luo ◽

Juxian Guo ◽

Hancai Chen ◽

Waheed Akram ◽

...

Keyword(s):

Candidate Gene ◽

Brassica Oleracea ◽

Fine Mapping ◽

Gene Analysis ◽

Whole Genome ◽

Genome Resequencing ◽

Chinese Kale ◽

Whole Genome Resequencing ◽

Yellow Petal ◽

Brassica Oleracea L

Download Full-text

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.

Download Full-text

Molecular dissection of resistance gene cluster and candidate gene identification of Pl17 and Pl19 in sunflower by whole-genome resequencing

Scientific Reports ◽

10.1038/s41598-019-50394-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Guojia Ma ◽

Qijian Song ◽

William R. Underwood ◽

Zhiwei Zhang ◽

Jason D. Fiedler ◽

...

Keyword(s):

Candidate Gene ◽

Gene Cluster ◽

Resistance Gene ◽

Snp Markers ◽

Reference Sequence ◽

Whole Genome ◽

Genome Resequencing ◽

Density Mapping ◽

Family Protein ◽

Whole Genome Resequencing

Abstract Sunflower (Helianthus annuus L.) production is challenged by different biotic and abiotic stresses, among which downy mildew (DM) is a severe biotic stress that is detrimental to sunflower yield and quality in many sunflower-growing regions worldwide. Resistance against its infestation in sunflower is commonly regulated by single dominant genes. Pl17 and Pl19 are two broad-spectrum DM resistance genes that have been previously mapped to a gene cluster spanning a 3.2 Mb region at the upper end of sunflower chromosome 4. Using a whole-genome resequencing approach combined with a reference sequence-based chromosome walking strategy and high-density mapping populations, we narrowed down Pl17 to a 15-kb region flanked by SNP markers C4_5711524 and SPB0001. A prospective candidate gene HanXRQChr04g0095641 for Pl17 was identified, encoding a typical TNL resistance gene protein. Pl19 was delimited to a 35-kb region and was approximately 1 Mb away from Pl17, flanked by SNP markers C4_6676629 and C4_6711381. The only gene present within the delineated Pl19 locus in the reference genome, HanXRQChr04g0095951, was predicted to encode an RNA methyltransferase family protein. Six and eight SNP markers diagnostic for Pl17 and Pl19, respectively, were identified upon evaluation of 96 diverse sunflower lines, providing a very useful tool for marker-assisted selection in sunflower breeding programs.

Download Full-text