No 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 BC 1 F 2:3 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%. Electronic supplementary material The online version of this article (10.1186/s12284-019-0305-y) contains supplementary material, which is available to authorized users.

Flash flooding imparts adverse effect on rice production worldwide. Because of the needs for multiple cropping and to avoid incidences of cold and diseases later in the season, early maturing submergence tolerant varieties have been urgently needed in some rice producing areas. Markerassisted backcrossing (MABC) was used to introgress the submergence-tolerance SUB1 QTL from BRRI dhan52 into a short-duration rice variety, BRRI dhan33. In this particular study, a combination of foreground and phenotypic selection was performed during the BC 1 F 1-BC 4 F 1 stages, while the whole set of foreground, recombinant and background markers were used at the BC 4 F 2 stage. At the final stage, the recovery of recipient parent genome ranged from 90.7 to 95.2% in 15 BC 4 F 3 promising lines. The introgression sizes of the different Sub1 lines were estimated to be around 2.4 to 5.6 Mb. The submergence tolerance of line BR9157-12-2-37-13-15-40 was found to be the best, having 87.7% survival. The grain yield of the Sub1 lines was also significantly higher compared with that of the original variety, BRRI dhan33, under both flooded and non-flooded conditions in on-station and on-farm trials. The maximum grain yield obtained from a BRRI dhan33-Sub1 line was 4.8 t/ha under on-farm non-flooded conditions and 3.8 t/ha under on-farm flooded conditions. The best selected Sub1 line may be released in the future as a short-duration, submergence-tolerant high-yielding variety for flood-prone rainfed areas in Bangladesh.