Rongsawat Thanyakorn, Pankasem Nattiwong, Thianthavon Tripop, Mangkalasane Piyamongkol, Aesomnuk Wanchana, Dumhai Reajina, Ruengphayak Siriphat, Siangliw Jonaliza L, Siangliw Meechai, Pitaloka Mutiara K, Xia Rui, Toojinda Theerayut, Ruanjaichon Vinitchan, Gray Julie E, Wanchana Samart, Arikit Siwaret
Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
BMC Plant Biol. 2025 Sep 2;25(1):1185. doi: 10.1186/s12870-025-07239-6.
Tiller number is a critical component of rice yield, as it directly influences overall productivity. While upland rice varieties are well adapted to lowland environments and prove resilient to fluctuating water availability, their typically low tillering capacity limits their performance in lowland ecosystems where conditions are more conducive to achieving higher yields.
To facilitate the marker-assisted selection (MAS) breeding of upland rice cultivars suitable for lowland conditions, we performed QTL-seq analysis using populations derived from a cross between a high-tillering lowland indica parent (PTT1) and a low-tillering upland tropical japonica line (NDCMP49). Two major QTLs associated with tiller number were identified on chromosomes 4 and 5 and designated as qTN4 and qTN5, respectively. Candidate gene analysis revealed NAL1 and OsOFP19 as putative genes underlying these loci. Functional validation of NAL1 using CRISPR-Cas9 knockout mutants confirmed its role as a negative regulator of tillering, as two independent alleles of nal1 mutant plants exhibited significantly increased tiller numbers compared with the wild type. Marker-trait association analysis further supported the additive effect of qTN4 (NAL1) and qTN5 (OsOFP19), indicating their potential for pyramiding in breeding programs. Functional KASP markers of NAL1 and OsOFP19 were developed and successfully validated in segregating populations, demonstrating their applicability for marker-assisted selection.
Collectively, these findings advance our understanding of the genetic regulation of tillering in rice and provide molecular tools for improving plant architecture and yield in upland rice varieties cultivated under lowland conditions.
分蘖数是水稻产量的关键组成部分，因为它直接影响整体生产力。虽然旱稻品种能很好地适应低地环境，并对波动的水分供应具有韧性，但其通常较低的分蘖能力限制了它们在条件更有利于实现高产的低地生态系统中的表现。
为了促进适合低地条件的旱稻品种的标记辅助选择（MAS）育种，我们使用高蘖数的低地籼稻亲本（PTT1）和低蘖数的旱稻热带粳稻品系（NDCMP49）杂交产生的群体进行了QTL-seq分析。在第4和第5染色体上鉴定出两个与分蘖数相关的主要QTL，分别命名为qTN4和qTN5。候选基因分析表明NAL1和OsOFP19是这些位点的推定基因。使用CRISPR-Cas9敲除突变体对NAL1进行功能验证，证实了其作为分蘖负调控因子的作用，因为nal1突变体植株的两个独立等位基因与野生型相比，分蘖数显著增加。标记-性状关联分析进一步支持了qTN4（NAL1）和qTN5（OsOFP19）的加性效应，表明它们在育种计划中聚合的潜力。开发了NAL1和OsOFP19的功能性KASP标记，并在分离群体中成功验证，证明了它们在标记辅助选择中的适用性。
总的来说，这些发现推进了我们对水稻分蘖遗传调控的理解，并为改善在低地条件下种植的旱稻品种的株型和产量提供了分子工具。
