Mishra Vagish, Dixit Shilpi, Tyagi Swati, Venkateswarlu Challa, Paul Pronob J, Gurjar Anoop Kishor Singh, Dixit Shalabh, Sandhu Nitika, Kurup Smita, Kumar Arvind, Sinha Pallavi, Singh Vikas Kumar, Singh Uma Maheshwar
International Rice Research Institute, Los Baños, Philippines.
IRRI South Asia Regional Center, Varanasi, Uttar Pradesh, India.
Front Plant Sci. 2025 Jan 29;15:1512234. doi: 10.3389/fpls.2024.1512234. eCollection 2024.
Water scarcity and labor shortage pose significant challenges in rice farming. Direct-seeded rice (DSR) is an efficient method that conserves water, reduces labor costs, and allows for full mechanization of cultivation. However, variable planting depth in undulated field leading to deep/shallow sowing of rice seeds during mechanical sowing presents a major hurdle, as existing varieties lack tolerance to deep sowing. To address this, a mapping population comprising 150 F lines, derived from MTU 1010 and AUS295, was developed and phenotyped for emergence from deep soil depth-related traits, including days of emergence (DE), percent germination (PG), mesocotyl length (ML), and coleoptile length (CL). The correlation revealed that DE has a significant negative correlation with PG, ML, and CL, whereas PG, ML, and CL are all positively correlated with each other. The mapping population was genotyped with mid-density SNP assay (1k-RiCA), and a linkage map was established with 414 polymorphic SNP markers. A total of 16 QTLs were identified for four traits, with phenotypic variance explained (PVE) ranging from 6.63% to 19.6% in the WS22. These included 5 QTLs for DE, 3 QTLs for PG, 4 QTLs for ML, and 4 QTLs for CL. Out of 16 QTLs identified, 12 were major effect QTLs ( , , , , , , , ) and 4 were minor effect QTLs ( ). During DS23 season, QTL analysis for DE and PG traits identified seven and three QTLs, respectively. Out of the ten QTLs identified in DS23 season, eight were stable across the season. This study reported 11 novel QTLs, while 7 had been previously reported. The study pinpointed three QTL hotspot regions: one on chromosome 1 ( , ) and two on chromosome 2 ( ) and ( ). Candidate gene analysis in the identified QTL regions found two genes associated with hormonal pathways: for gibberellin signaling and for abscisic acid signaling. Additionally, one gene () associated with early seedling vigor and another () regulates germination through coleoptile growth. The identified QTLs, genes, and breeding lines from this study provide valuable resources for developing rice varieties with enhanced tolerance to deep soil emergence, making them well-suited for mechanized DSR systems.
水资源短缺和劳动力短缺给水稻种植带来了重大挑战。直播水稻是一种节水、降低劳动力成本并实现种植全程机械化的高效方法。然而，在起伏不平的田地里，机械播种时水稻种子的播种深度不一，导致深播或浅播，这是一个主要障碍，因为现有品种缺乏耐深播性。为了解决这个问题，构建了一个由150个F系组成的作图群体，这些F系源自MTU 1010和AUS295，并对与深土层出苗相关的性状进行了表型分析，包括出苗天数（DE）、发芽率（PG）、中胚轴长度（ML）和胚芽鞘长度（CL）。相关性分析表明，DE与PG、ML和CL呈显著负相关，而PG、ML和CL之间均呈正相关。利用中密度SNP分析（1k-RiCA）对该作图群体进行基因分型，并构建了包含414个多态性SNP标记的连锁图谱。共鉴定出与四个性状相关的16个QTL，在WS22中，表型变异解释率（PVE）为6.63%至19.6%。其中包括5个与DE相关的QTL、3个与PG相关的QTL、4个与ML相关的QTL和4个与CL相关的QTL。在鉴定出的16个QTL中，12个是主效QTL（ ， ， ， ， ， ， ， ），4个是微效QTL（ ）。在DS23季节，对DE和PG性状进行QTL分析，分别鉴定出7个和3个QTL。在DS23季节鉴定出的10个QTL中，有8个在整个季节都稳定。本研究报道了11个新的QTL，其中7个此前已有报道。该研究确定了三个QTL热点区域：一个在1号染色体上（ ， ），两个在2号染色体上（ ）和（ ）。在鉴定出的QTL区域进行候选基因分析，发现了两个与激素途径相关的基因：一个与赤霉素信号传导有关（ ），另一个与脱落酸信号传导有关（ ）。此外，一个与幼苗早期活力相关的基因（ ）和另一个通过胚芽鞘生长调节发芽的基因（ ）。本研究鉴定出的QTL、基因和育种系为培育耐深土层出苗能力增强的水稻品种提供了宝贵资源，使其非常适合机械化直播水稻系统。
