Product introduction

Genome wide association study (GWAS) is a genome-wide statistical analysis method for mining genes influencing phenotypic traits through high-density single nucleotide polymorphisms (SNPs) and exploiting linkage disequilibrium. For species groups with existing reference genomes, whole-genome resequencing can accurately obtain genome-wide genetic information and maximize the genetic variation within the group, which helps to study the molecular regulatory mechanisms of typical traits of the species under study and provides important scientific theoretical and practical applications for molecular breeding and domestication improvement.

The advantages of the high-quality map of fungal genome

(1) Genome-wide level, more complete and dense variation information;
(2) Abundant types of genetic variation: single nucleotide polymorphisms (SNP), insertion
deletions (InDel), structural variation (SV) and copy number variation (CNV), with in-depth analysis of all aspects of genetic variation;
(3) High resolution, up to single base level;
(4) Pinpointing candidate genes or gene regions associated with traits.

Analysis content

 

Classic case: 

Title: Resequencing of 243 diploid cotton accessions based on an updated a genome identifies the genetic basis of key agronomic traits.
 
Journal: Nature Genetics (IF = 38.330)
 
Background: Cotton is one of the world's most important cash crops and an important resource for the study of plant polyploidy. the ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for modern cultivated allotetraploid cotton. g. arboreum may have been domesticated in Madagascar or the Indus basin and subsequently spread to Africa and other parts of Asia. It was first introduced to China about 1000 years ago as an ornamental plant. Although cotton breeders have constructed various RFLP5 and SSR-based genetic maps, key genes associated with excellent agronomic and economic traits of G. arboreum and G. herbaceum have not been identified.
 
Key findings:

The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.
 

Publication

Du XM, Huang G, Li FG et al. Resequencing of 243 diploid cotton accessions based on an updated a genome identifies the genetic basis of key agronomic traits. Nature Genetics, 2018.