Simultaneous Improvement and Genetic Dissection of Salt Tolerance of Rice (Oryza sativa L.) by Designed QTL Pyramiding

Breeding of multi-stress tolerant rice varieties with higher grain yields is the best option to enhance the rice productivity of abiotic stresses prone areas. It also poses the greatest challenge to plant breeders to breed rice varieties for such stress prone conditions. Here, we carried out a designed QTL pyramiding experiment to develop high yielding “Green Super Rice” varieties with significantly improved tolerance to salt stress and grain yield. Using the F4 population derived from a cross between two selected introgression lines, we were able to develop six mostly homozygous promising high yielding lines with significantly improved salt tolerance and grain yield under optimal and/or saline conditions in 3 years. Simultaneous mapping using the same breeding population and tunable genotyping-by-sequencing technology, we identified three QTL affecting salt injury score and leaf chlorophyll content. By analyzing 32M SNP data of the grandparents and graphical genotypes of the parents, we discovered 87 positional candidate genes for salt tolerant QTL. According to their functional annotation, we inferred the most likely candidate genes. We demonstrated that designed QTL pyramiding is a powerful strategy for simultaneous improvement and genetic dissection of complex traits in rice

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Background:Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity andgreatly affect rice yield and quality. To improve rice production, understanding the genetic and molecularresistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is aneffective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the geneticrelationship between them in a genetically diverse population.Results:A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW),shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe orSZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a,qSdw3b,qSdw12andqSFe5/qSZn5) were detected in the same genomic regions under the two stress conditionsand 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses.Conclusion:Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidategenes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information forfuture functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assistedselection or designed QTL pyramiding