Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (qSUB3), 4 (qSUB4), 6 (qSUB6-1 and qSUB6-2), 11 (qSUB11-1, qSUB11-2 and qSUB11-3), and 12 (qSUB12-1 and qSUB12-2). Two candidate genes (Os03g0679300 and Os11g0517800) in the two QTL regions associated with submergence tolerance were detected. The results of this study provide associated SNPs in candidate genes for submergence condition and strategies for developing submergence condition in breeding programs.

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• Comprehensive Evaluation of Cold and Anaerobic Tolerance in Rice Oryza sativa L. and Screening of Multistress‐Resistant Germplasm
  Jianghui Yu, Shaoran Suo, Cheng Zheng, Ling Liu, Yunpeng Peng, Huang Zhou, Zhijun Wang, Huan Cao, Yongkang Liu, Xiwen Shi, Dingyang Yuan, Meijuan Duan
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• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
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The SUBMERGENCE 1 (SUB1) locus, conferring tolerance to complete inundation, was identified, and gel-based DNA markers, AEX1 and GnS2, were previously developed for marker-assisted breeding (MAB). However, a high throughput and high specific method, at low cost, is still required to detect Sub1 alleles. Kompetitive Allele Specific PCR (KASP) markers enable high throughput analysis for a large number of seeds, as well as detection of both alleles, in a single reaction. In this study, we developed KASP markers that can distinguish specific alleles at Sub1A loci based on single nucleotide polymorphisms (SNPs). Marker validations were carried out by genotyping of a segregating population with the developed KASP markers. The results from KASP assay and gel-based marker analysis were consistent for Sub1A alleles. KASP markers developed for Sub1A would be helpful due to high accuracy, low cost, and a high throughput genotyping feature in MAB.

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• Identification of KASP-SNP markers correlated with both growth and hypoxia tolerance traits in blunt snout bream (Megalobrama amblycephala)
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The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of SUB1, an FR13A-derived QTL conferring submergence tolerance at the vegetative stage, using marker-assisted backcrossing (MABC). Ciherang-Sub1, one of these improved near isogenic lines (NILs), showed significantly higher tolerance compared to the original cultivar while retaining its desirable agronomic qualities. However, due to the current shift to direct seeding, seed germination may also be adversely affected by flooding; thus the addition of major QTLs which can confer anaerobic germination (AG) tolerance will be highly beneficial. The AG tolerance QTL, qAG-9-2, also referred to as AG1, derived from Khao Hlan On, a Myanmar landrace, has been introgressed into the elite cultivar IR64 to produce IR64-AG1. This research focused on the transfer of AG1 to Ciherang-Sub1 via MABC, using IR64-AG1, a closely-related donor. Introgression of AG1 and recovery of the Ciherang genome was done in two backcross generations followed by one generation of selfing. The use of a closely-related donor shortened the development period to two years which could have been further reduced if a larger BC₁F₁ population had been used. Phenotypic evaluation showed that introgression of AG1 significantly increased AG tolerance compared to Ciherang-Sub1, and that the newly developed Ciherang-Sub1+AG1 retained the submergence tolerance from SUB1. The approach is very promising for faster development of improved lines using closely-related cultivars or improved lines as donors for introducing key traits.

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