# Genetic Diversity Analysis of Cotton Cultivars Using a 40K Liquid Chip in Northern Xinjiang

## TL;DR

This study analyzes the genetic diversity of cotton cultivars in Northern Xinjiang using a 40K SNP chip, revealing a narrow genetic base and the influence of a specific US variety.

## Contribution

The study provides new insights into the genetic structure and breeding history of cotton cultivars in Northern Xinjiang using high-density SNP markers.

## Key findings

- 83 cotton materials were grouped into three subgroups based on genetic diversity and kinship analysis.
- The introduced US variety 'Beiersinuo' significantly influenced local breeding, leading to a narrow genetic base.
- SNP markers revealed an average kinship coefficient of 0.72 among Northern Xinjiang cotton varieties.

## Abstract

Genetic diversity and kinship information of cotton germplasm resources are fundamental to breeding, providing a theoretical basis for the rational selection of hybrid parents and further breeding of new varieties with high yield, high quality, and multi-resistance. This study utilized cotton varieties that have been used for variety improvement or are widely planted in the Northern Xinjiang cotton region as materials. Genotyping was performed using the ZJU CottonSNP40K chip to analyze genetic diversity and kinship relationships. A total of 26,852 high-quality SNP markers were obtained, including 15,222 SNPs in subgenome A and 11,630 SNPs in subgenome D. The number of SNPs per chromosome ranged from 547 (A04) to 2168 (A08). Based on phylogenetic tree and principal component analysis, the 83 materials were clustered into 3 major subgroups. Group I contained varieties introduced from the former Soviet Union and the United States, which have become important parents for cotton breeding in Northern Xinjiang. Among them, as many as 27 varieties were derived and selected from the introduced US variety ‘Beiersinuo’ as a parent. While playing an important role in cotton breeding in Northern Xinjiang, this has also led to the current situation where the genetic base of Northern Xinjiang varieties is relatively narrow (average kinship coefficient 0.72). It clarifies the significant role of introduced American variety ‘Beiersinuo’ in the breeding of Northern Xinjiang cultivars and provides theoretical guidance for broadening the genetic base of Northern Xinjiang cotton varieties.