Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China

Author:

Hang Yu,Yue Liu,Bingrui Sun,Qing Liu,Xingxue Mao,Liqun Jiang,Shuwei Lyu,Jing Zhang,Pingli Chen,Dajian Pan,Wenfeng Chen,Zhilan Fan,Chen Li

Abstract

AbstractAs the pioneer of the Green Revolution in China, Guangdong province witnessed the improvement and spread of semi-dwarf Xian/Indica rice cultivars and possessed diverse rice germplasm of landrace and cultivars. A total of 517 accessions containing a core germplasm of 479 newly sequenced landraces and modern cultivars were used to reveal breeding signatures and key variations for regional genetic improvement of indica rice from Guangdong. Four subpopulations were identified in the collection, which including Ind IV as a novel subpopulation that not covered by previously released accessions. Modern cultivars of subpopulation Ind II were inferred to have less deleterious variations, especially in yield related genes. About 15 Mb genomic segments were identified as potential breeding signatures by cross-population likelihood method (XP-CLR) of modern cultivars and landraces. The selected regions spanning multiple yield related QTLs (quantitative trait locus) which identified by GWAS (genome-wide association studies) of the same population, and specific variations that fixed in modern cultivars of Ind II were characterized. This study highlights genetic differences between traditional landraces and modern cultivars, which revealed the potential molecular basis of regional genetic improvement for Guangdong indica rice from southern China.

Funder

Natural Science Foundation of Guangdong Province

Special Funds for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science

Guangzhou Science and Technology Plan Project

The Project of Collaborative Innovation Center of GDAAS

Seed Industry Revitalization Project of Special Fund for Rural Revitalization Strategy in Guangdong Province

Key Field Research and Development Project of Guangdong Province

Publisher

Springer Science and Business Media LLC

Subject

Plant Science,Soil Science,Agronomy and Crop Science

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