Targeted association analysis identified japonica rice varieties achieving Na+/K+ homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra

Abstract

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na(+) concentration and Na(+)/K(+) equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na(+) concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement.

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

“…The physiological similarity of drought and salt tolerance is the osmotic tolerance or ability to cope with low water potential (Nguyen et al 1997;Ahmadi et al 2011). Apart from this, rice salt tolerance depends on the control of salt uptake and exclusion from growing tissues (Ahmadi et al 2011). In this study, the genetic relationships of rice seed germination and seedling Fig.…”

“…and Cl -on the inhibition of seed germination under salt stress condition (Wang et al 2011b). The physiological similarity of drought and salt tolerance is the osmotic tolerance or ability to cope with low water potential (Nguyen et al 1997;Ahmadi et al 2011). Apart from this, rice salt tolerance depends on the control of salt uptake and exclusion from growing tissues (Ahmadi et al 2011).…”

“…A large number of quantitative trait loci (QTLs) for seed germination and seedling growth under normal (Cui et al 2002;Zhang et al 2005;Wang et al 2010;Li et al 2011;Cheng et al 2013Cheng et al , 2014, drought (Teng et al 2002;Zhou et al 2006;Kamoshita et al 2008;Hu et al 2011;Ding et al 2011) and salt (Pandit et al 2010;Ahmadi et al 2011;Tian et al 2011;Wang et al 2011b;Cheng et al 2012;Wang et al 2012a, b) conditions have been identified by the traditional biparental mapping approach in rice. However, the genetic relationship of seed germination and/or seedling growth between multiple conditions at the whole-genome level is still unclear.…”

“…Rice (Oryza sativa L.) is rated as a drought-and saltsensitive crop (Ahmadi et al 2011;Swamy et al 2013). The frequent occurrence of drought and salt stress has been identified as the most widespread soil problem in rice production.…”

Dynamic QTL analysis of the Na⁺ content, K⁺ content, and Na⁺/K⁺ ratio in rice roots during the field growth under salt stress

“…The plant root has a remarkable ability to control its Na + and K + content and to regulate their uptake and transport to the shoot (Munns 2005). However, this ability is variable in different plant species and cultivars, and the ability to maintain a low Na + /K + ratio is a key feature of the salt tolerance (Ahmadi et al 2011).…”