Genes, Vol. 15, Pages 378: Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement

Genes, Vol. 15, Pages 378: Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement Genes doi: 10.3390/genes15030378 Authors: Shang Liu Hailiang Cheng Youping Zhang Man He Dongyun Zuo Qiaolian Wang Limin Lv Zhongxv Lin Guoli Song Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort’s fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that se...
Source: Genes - Category: Genetics & Stem Cells Authors: Tags: Article Source Type: research