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 Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

2021 ◽  
Author(s):  
Huang Li ◽  
Xiao Hu ◽  
John T. Lovell ◽  
Paul P. Grabowski ◽  
Sujan Mamidi ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Natural Variation ◽  
Whole Genome ◽  
Genetic Dissection ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

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.

Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Lei-Lei Li ◽  
Shi-Ke Ma ◽  
Wei Peng ◽  
You-Gui Fang ◽  
Hai-Rui Duo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Sheep Breeds ◽  
Tibetan Sheep ◽  
Whole Genome Resequencing

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

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.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 959
Author(s):  
Alexander Igoshin ◽  
Nikolay Yudin ◽  
Ruslan Aitnazarov ◽  
Andrey A. Yurchenko ◽  
Denis M. Larkin
Keyword(s):  
Body Temperature ◽  
Cold Stress ◽  
Candidate Snps ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Functional Annotations ◽  
Cold Environments ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Whole Genome Resequencing

Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.

scholarly journals High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut

2021 ◽  
Author(s):  
Yifei Jiang ◽  
Huaiyong Luo ◽  
Bolun Yu ◽  
Yingbin Ding ◽  
Yanping Kang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Aspergillus Flavus ◽  
Genetic Linkage ◽  
Genetic Basis ◽  
Genetic Linkage Map ◽  
Aflatoxin Contamination ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Favorable Alleles ◽  
Whole Genome Resequencing

Abstract Cultivated peanut (Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

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