Due to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constructed a collection of recombinant inbred lines (RIL) comprising 275 lines derived from the H335 and CHA-1 cross by the method of single seed descent. Via a genotyping-by-sequencing (GBS) strategy, a high-density genetic map containing 2498 recombination bin markers was constructed, the average physical distance between the markers was only 149.38 Kb. After anaerobic treatment, 12 phenotypes related to both the coleoptile at germination and seedling quality at budding were evaluated. There were no significant correlations between seedling and bud traits. Genetic mapping of quantitative traits was performed for these traits across two cropping seasons. A total of 20 loci were detected, named locus 1~20. Three of them were repeatedly detected across both seasons. Six loci overlapped with those in previous reports, and nine loci were associated with multiple traits at both stages. Notably, locus 3, which is located on chromosome 2 (26,713,837 to 27,333,897 bp), was detected for both the germination and bud traits. By focusing on the locus 3 interval and by combining gene annotation and expression analyses, we identified a promising candidate gene, trehalose-6-phosphate phosphatase (OsTPP1, LOC_Os02g44230). Furthermore, RILs (G289, G379, G403, G430 and G454) that have superior phenotypes and that pyramid elite alleles were recognized. The findings of present study provide new genetic resources for direct-seeding rice (DSR) varieties for molecular breeding strategies and expand our knowledge of genetic regulation of seedling establishment under anaerobic conditions.
Reduced temperatures during germination adversely affect rice (Oryza sativa L.) production. Little is known, however, of the genes or genetic loci involved.Here, QTLs were investigated in a recombinant inbred line (RIL) resulting from a 02428 (japonica)-YZX (indica) cross. The phenotypes of the cultivars differ significantly when exposed to low temperatures during germination. Mapping with a high-density bin map identified 11 loci associated with low-temperature germination of which loci 2 and 4 were identified by multiple traits over two seasons.Locus 2 was a major genetic locus, explaining 22.36% of phenotypic variation.The haplotype results showed that the pyramiding of favorable alleles of these two loci was beneficial to improving the rice seeds' low-temperature germinability. RNA-seq analysis was performed on the second day of germination at low temperature for both parents. Three DGEs (Os03g0119800, Os03g0120900, and Os03g0121300) were obtained for locus 2 and were confirmed as the most likely candidates by qRT-PCR verification, gene sequence alignment, and haplotype analysis. Collectively, these quantitative trait loci and candidate genes may be valuable for the breeding of cold-tolerant rice lines as well as broadening our knowledge of the genetics underlying germination at low temperatures.
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