Thai jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant

Abstract

Submergence tolerance is an important agronomic trait for rice grown in South-East Asia, where flash flooding occurs frequently and unpredictably during the monsoons. Although mapping locations of one major and several minor quantitative trait loci (QTL) were known previously, improving submergence tolerance in agronomically desirable types of rice has not been achieved. KDML105 is jasmine rice widely grown in rain-fed lowland regions of Thailand. This cultivar is very intolerant of submergence stress. To improve submergence tolerance in this cultivar, three submergence-tolerant cultivars, FR13A, IR67819F2-CA-61 and IR49830-7-1-2-2, were cross-pollinated with KDML105. Transferring the major QTL for submergence tolerance was facilitated by four back-crossings to the recipient KDML105. Molecular markers tightly linked to the gene(s) involved were developed to facilitate molecular genotyping. We demonstrated that individuals of a BC4F3 line that retained a critical region on chromosome 9 transferred from tolerant lines were also tolerant of complete submergence while retaining all the agronomically desirable traits of KDML105. In addition, effects of secondary QTLch2 were detected statistically in back-cross progenies. Effects of secondary QTLch7 were not statistically significant. The close association between tightly linked markers of the tolerance locus on chromosome 9 and submergence tolerance in the field demonstrates the considerable promise of using these markers in lowland rice breeding programmes for selecting increased submergence tolerance.

Fig. 1. Distribution in BC4 progeny of plant elongation during submergence (cm) and plant survival (% of each line) after experiencing 10 d submergence stress. Tests were made in the year 2000 on each back‐cross (FR × KD, DH × KD and IR × KD). The frequency axes refer to the number of lines falling in each elongation or survival class.

Fig. 2. Graphical genotypes of the most tolerant and susceptible BC4F2 progenies in the SubQTL region on the short arm of rice chromosome 9. Distances are in kilobases (kb). Trait descriptions were specified in Materials and Methods. ‘nd’ refers to no data. The picture at the top shows the appearance of a promising submergence‐tolerant BC line (no. 873) after 10 d submergence.