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

Sep 30, 2026

Upload by Mabel

Genetic diversity and kinship information underpin cotton breeding by enabling rational hybrid-parent selection and the development of high-yield, high-quality, and multi-resistant varieties. The study analyzed cotton varieties used in improvement and widely grown in Northern Xinjiang. Genotyping was conducted with the ZJU CottonSNP40K chip to quantify diversity and kinship, yielding 26,852 high-quality SNP markers across subgenomes A and D. Phylogenetic and PCA clustering grouped 83 materials into three major subgroups. Results show U.S. and former Soviet introductions, including a major contribution from the American variety ‘Beiersinuo’, while also revealing a relatively narrow genetic base.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Abstract

Introduction

Article Genetic Diversity Analysis of Cotton Cultivars Using a 40K Liquid Chip in Northern Xinjiang Zhihong Zheng 1,†, Ningshan Wang 1,†, Shangkun Jin 2, Kewei Ning 1, Guoli Feng 1, Haiqiang Gao 1, Zhanfeng Si 2, Tianzhen Zhang 2 and Nijiang Ai 1, * Academic Editor: Nunzio D’Agostino Received: 5 November 2025 Revised: 10 December 2025 Accepted: 10 December 2025 Published: 5 January 2026 Copyright: © 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. 1 Shihezi Academy of Agricultural Sciences, Shihezi 832000, China 2 Modern Seed Industry Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China * [Correspondence: xjshznykxyjy@163.com](Correspondence: xjshznykxyjy@163.com) † These authors contributed equally to this work. 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’ asa 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. Keywords: ZJU CottonSNP40K; Northern Xinjiang cotton varieties; genetic relationship 1. Introduction Xinjiang is China’s most important high-quality commercial cotton production base. Based on climatic conditions, the Xinjiang cotton region is generally divided into the Northern Xinjiang early-maturing cotton region and the Southern Xinjiang early-to-mediummaturing cotton region. The Northern Xinjiang early-maturing cotton region holds an extremely important position in Xinjiang’s high-quality cotton production, accounting for 30% of the total planting area and over 32% of the total product in in Xinjiang. The Northern Xinjiang cotton production area boasts superior farmland infrastructure, high mechanization levels, advanced irrigation techniques, and high cultivation management standards, with a favorable market for the cotton industry. Over the years, the “Xinluzao” series varieties have become the dominant cultivars in this region across different periods due to their good early maturity, high yield, and stability, making outstanding contributions to cotton production development in Northern Xinjiang. Analyzing the genetic diversity and kinship relationships of cotton cultivars is of great significance for promoting the breeding of new cotton varieties suitable for the Northern Xinjiang cotton region with early maturity, high yield, superior quality, and multi-resistance. In-depth research on the genetic divers

FAQs

What is the purpose of genetic diversity and kinship analysis in cotton breeding?

It provides a theoretical basis for selecting rational hybrid parents and for developing new varieties with high yield, high quality, and multi-resistance.

Which genotyping platform and marker type were used in the study?

The study used the ZJU CottonSNP40K SNP chip to genotype cotton materials and analyze genetic diversity and kinship relationships.

How were the 83 cotton materials grouped in the analysis?

Phylogenetic tree and principal component analysis clustered the 83 materials into three major subgroups.

Sep 30, 2026

Upload by Mabel