Abstract
Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BC1F2:3 mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6–1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1–1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.
Highlights
The ability of rice to germinate under water is generally low
We identified a set of eight lines with different combinations of the three major Quantitative Trait Loci (QTL) identified in this study, white-colored pericarp and high germination under aerobic and anaerobic conditions (Table 5)
Tolerant alleles for all three QTLs were contributed by Kalarata
Summary
The ability of rice to germinate under water is generally low. Most modern rice varieties either fail completely to germinate under water or fail to elongate the coleoptile and develop roots and shoots for further development under a long period of oxygen deprivation, resulting in partial to complete crop failure (Magneschi and Perata, 2009; Narsai et al, 2015). Genetic variation exists among rice varieties for anaerobic germination (AG), with some landraces being able to germinate under water A series of linkage mapping studies identified many QTLs with major and minor effects on AG (Jiang et al, 2004; Jiang et al, 2006; Angaji et al, 2010; Septiningsih et al, 2013; Baltazar et al, 2014). One of these QTLs, qAG9–2 on chromosome 9, has been fine-mapped to OsTPP7, which is responsible for starch mobilization to drive embryo germination and coleoptile elongation (Kretzschmar et al, 2015). The exploration of novel QTLs for tolerance of anaerobic conditions during germination is essential to understand the genetics and molecular basis of tolerance and to provide robust QTL targets for marker-assisted breeding
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