Recent Advances in Genomics, Genetic Resources Evaluation and Breeding of Rice

A Special Issue of Agronomy (ISSN 2073-4395) belonging to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 28 February 2027 | Viewed by 1894

Editors


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Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: rice biotic and abiotic stress; gene identification; genetic resource evaluation; genomic selection; omit study; genomic breeding

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Guest Editor
College of Agriculture, Yangtze University, Jingzhou 434025, China
Interests: rice germplasm; gene discovery; rice yield and quality; genomic breeding; gene function analysis

Special Issue Information

Dear Colleagues,

Rice is one of the most important staple crops in the world. With the increase in the global population and worsening climate change, rice yield should largely be increased to meet consumer demand. Moreover, in line with increases in living standards, rice quality also should be improved. In recent years, significant advances have been made in rice genomics and genetics, including whole-genomic sequencing, bioinformatics, genomic selection, molecular technologies, marker-assisted selection, and genetic resources development, resulting in the identification of many important genes essential for rice yield and quality, and a series of green, higher-yield, and superior quality varieties have been bred and cultivated worldwide. This Special Issue of Agronomy will highlight the latest advances in genetic resources evaluation; the mining of rice genes important for rice yield, quality biotic and abiotic stress, and other traits via QTL mapping and genome-wide association studies; gene function analysis; novel genetic resource development; whole-genomic sequencing; bioinformatics studies; omics studies; and rice variety breeding.

Dr. Kai Chen
Dr. Xianjin Qiu
Guest Editors

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Keywords

  • rice yield and quality
  • rice biotic and abiotic traits
  • genetic resource evaluation development
  • gene identification
  • gene function analysis
  • omics study
  • whole-genome sequencing
  • bioinformatics study
  • genomic selection
  • novel variety breeding

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Published Papers (1 paper)

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Research

18 pages, 562 KB  
Article
Genetic Dissection of Yield-Related Traits Using an Inter-Subspecific Chromosome Segment Substitution Line Population in Rice
by Yongle Xu, Yue Pan, Yong Xiang, Yue Sun, Junying Xu, Haiyang Liu, Longwei Yang, Zhilian Qi, Xinxin Tang, Famao Liang, Hui Hu, Xianjin Qiu and Jian Yu
Agronomy 2026, 16(5), 580; https://doi.org/10.3390/agronomy16050580 - 7 Mar 2026
Viewed by 709
Abstract
Rice yield is a complex quantitative trait. Although a lot of genes for yield have been cloned, their genetic basis remains unknown. In the present study, a set of chromosome segment substitution line population (CSSL) was developed, derived from the indica variety Huanghuazhan [...] Read more.
Rice yield is a complex quantitative trait. Although a lot of genes for yield have been cloned, their genetic basis remains unknown. In the present study, a set of chromosome segment substitution line population (CSSL) was developed, derived from the indica variety Huanghuazhan as the recipient parent and the Aus variety N22 as the donor parent, and a high-density bin map containing 609 bins was constructed by resequencing. The CSSL population comprised 155 families with an average background recovery rate of 93.02%. Nine yield-related traits, including plant height, panicle number, panicle length, primary branch number, spikelet number per panicle, grain number per panicle, seed setting rate, 1000-grain weight, and grain yield per plant, were evaluated across four environments. The results showed significant differences in yield-related traits between the two parents across four environments. All nine traits showed continuous distribution with transgressive segregation. Spikelet number per panicle, grain number per panicle and 1000-grain weight showed strong correlations with each other, whereas panicle number had weak correlations with them. A total of 80 main-effect quantitative trait loci (QTLs) affecting yield-related traits were identified, among which 13 QTLs were repeatedly detected in multiple environments, 45 QTLs were located in 8 pleiotropic QTL regions, and 47 QTLs showed significant interactions with environments. In addition, 260 pairs of epistatic QTLs underlying yield-related traits were identified, of which 2 pairs stably expressed across different environments, and 11 pairs controlled more than two traits. These findings provide a theoretical basis for clarifying the genetic differentiation between indica and Aus and cloning yield-related genes, and offer valuable gene resources for molecular breeding of high-yield rice varieties. Full article
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