QTL mapping and effect confirmation for anaerobic germination tolerance derived from the japonica weedy rice landrace PBR

Abstract

As one of the main rice establishment methods, direct seeding has the advantages of saving labour and reducing costs for farmers. However, the expansion of direct seeding has been constrained by poorly levelled fields, heavy rainfall and poor drainage after sowing. The development of cultivars with anaerobic germination tolerance could improve or overcome these shortcomings of most rice under flooding conditions. In this study, a japonica‐type rice with anaerobic germination tolerance was suggested as a new genetic source and QTL analysis was carried out to improve adaptation to direct seeding. Three QTLs, qAG1, qAG3 and qAG11, were identified, explaining 13.44%, 6.71% and 14.52% of the phenotypic variance, respectively. In an evaluation of the most effective QTL combination, two QTL combinations (qAG1NP + qAG3PBR + qAG11PBR and qAG1NP + qAG11PBR) showed stable survival rates under submergence of filed condition. Based on the results, we will characterize the candidate genes within the detected target regions in further research, and the lines with advantageous alleles will be used to develop reliable cultivars to support the wide adoption of direct‐seeding practices in japonica rice.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

“…The Korean weedy rice, photoblastic rice (PBR), was identified with potential for anaerobic condition survivability with high germination percentage [ 104 ]. Jeong et al [ 105 ] developed a mapping population using PBR, and the authors reported three QTLs involved in imparting tolerance of flooding: qAG1 , qAG3 , and qAG11 . Other genes have also been reported, such as the QTLs qAG-9–2 ( AG1 ) and qAG-7–2 ( AG2 ) [ 106 ].…”

Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice

“…A novel QTL ( qACE3.1 ) was identified for coleoptiles elongation under anaerobic condition in the population of chromosome segment substitution lines (CSSL S ) substituted with Koshihari in IR64 genetic background [ 130 ]. Three QTLs ( qAG1 , qAG3 and qAG11 ) were identified from a study carried out by Jeong et al [ 131 ] by using 188 RILs from a cross between PBR (Photo-blastic Rice) as a donor and ‘Nampyeong’, a Korean japonica cultivar. Among different anaerobic germination QTLs identified till now, the QTL ( qAG.9.2 ) is pinned down to AG1 gene, responsible for coleoptile elongation during anaerobic germination.…”

How Can Weedy Rice Stand against Abiotic Stresses? A Review

“…Submergence tolerance is another characteristic greatly variable in weedy rice, while in many cultivated varieties poor seedling establishment often occurs in case of heavy rainfall, poor drainage or in uneven field levelling [112]. The unfavorable submergence conditions may result in high yield losses in rice [112].…”

“…Submergence tolerance is another characteristic greatly variable in weedy rice, while in many cultivated varieties poor seedling establishment often occurs in case of heavy rainfall, poor drainage or in uneven field levelling [112]. The unfavorable submergence conditions may result in high yield losses in rice [112]. During flooding, seeds have to germinate in low aerobic conditions, which limit the respiration, creating an unsuitable environment for germination and seedling growth [113].…”

“…However, the variability of weedy rice in flooding tolerance is great and some populations can be more tolerant to flooding than cultivated rice [114]. Specific genes regulating submergence tolerance in weedy rice can be used in breeding program to improve rice varieties [112,115].…”