Genomics Applications to Salinity Tolerance Breeding in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 31

Chapter 3

Genomics Applications to Salinity Tolerance
Breeding inRice

J.DamienPlatten,MichaelJ.Thomson,and AbdelbagiM.Ismail

Abstract

Salinity tolerance is a complex trait, and it is typical for 5 to 8 significant quantitative trait loci
(QTLs) to be identified in most mapping populations, and for many of these loci to control a relatively
small proportion (15-30%) of the total phenotypic variance. Comparisons of QTLs across multiple
populations and from multiple donors show that many QTL regions are shared between traditional
donors, yet to date only a single gene ( OsHKT1.5 ) has been shown to confer a QTL phenotype
( qSKC1 ) in rice through map-based cloning. The slow progress in cloning these QTLs is partly due
to large QTL intervals, a consequence of the expense of mapping larger populations, and partly due
to the large number of genes that could potentially confer salinity tolerance annotated at each locus.
However, the availability of cheap high-throughput sequencing and SNP genotyping technologies
stands to revolutionize this process by providing unprecedented marker density. The high level of
marker density should make association mapping feasible, thus freeing QTL discovery from the
need to produce mapping populations. Second, QTL intervals derived from association mapping are
much smaller, thus greatly aiding in narrowing the list of candidate genes. Third, the availability of
whole-genome de novo or resequencing data makes it feasible to sort through candidate genes found
in even quite large QTL intervals. The combined effect of these factors should greatly reduce the
time and effort required to investigate the genetics of salinity tolerance in rice, with the corollary that
the focus of research efforts is likely to shift towards producing accurate, detailed phenotype data
and towards validation efforts for identified loci. At the same time, major QTLs for tolerance can be
rapidly transferred through marker-assisted backcrossing (MABC) to develop improved varieties for
salt-stressed environments. Likewise, as more genomics data lead to improved characterization of the
genes and alleles controlling salinity tolerance, progress towards successful molecular breeding can
be accelerated.

Introduction

not naturally have strong tolerance mechanisms
against salinity (Flowers et al. 2010). Salinity
is a historic problem for agriculture, and as

The majority of domesticated crops did not
evolve in areas affected by salt stress and do