Chinese Journal OF Rice Science >
Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice
#These authors contributed equally to this paper
Received date: 2024-01-09
Revised date: 2024-02-06
Online published: 2025-03-19
【Objective】Based on advances in rice functional genomics, this study aimed to screen favorable alleles of the Gn1a gene controlling grain number per panicle, providing technical support for modern rice variety improvement. 【Method】Advanced genetic populations were developed through backcrossing and self-crossing for QTL mapping. Near-isogenic lines (NILs) were constructed to validate QTL effects. Target gene sequences were amplified and aligned, followed by designing functional markers for genotyping. 【Result】A major quantitative trait locus (QTL) controlling secondary branch number and grains per panicle was co-localized with the Gn1a locus on chromosome 1 short arm. This mapping utilized four BC3F3 populations derived from crosses between the japonica donor parent Jizi 1560 and recurrent parents, including early indica varieties (Zhongjiazao 17, Zhongzao 39) and three-line restorer lines (Huazhan, R173). Sequence analysis revealed an unreported indica-specific allele (Gn1a-i) in Zhongjiazao 17 and Zhongzao 39, characterized by a 16-bp deletion in the 5' UTR compared to the japonica allele (Gn1a-j). Comparative analyses of four near-isogenic line (NIL) populations confirmed that Gn1a-i significantly increased grains per panicle and yield. A functional marker (ZC51) targeting the 16-bp deletion was developed to genotype 39 rice materials, which were categorized into nine types: conventional early/late indica varieties, three-line maintainers/restorers, two-line sterile lines, northern/southern japonica varieties, landraces, and wild rice. All modern indica materials (cultivars and hybrid parents) carried Gn1a-i, whereas landraces and wild rice retained Gn1a-j. Notably, both southern and northern japonica varieties exhibited biallelic Gn1a-i and Gn1a-j. 【Conclusion】It was confirmed that Gn1a-i allele increased grain yield by increasing number of primary branches, secondary branches and grains per panicle. The favorable allele of Gn1a-i has great potentials in the improvement of japonica rice varieties, and the functional gene marker of ZC51 can be directly used in the marker-assisted selection of Gn1a.
LIU Zhichao, CHANG Longxue, AI Xin, JIN Long, ZHANG Fengyong, LI Zhiyong, WANG Yifeng, TONG Xiaohong, HUANG Jie, ZHANG Jian, JIN Jian, YING Jiezheng . Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice[J]. Chinese Journal OF Rice Science, 2025 , 39(2) : 220 -230 . DOI: 10.16819/j.1001-7216.2025.240105
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