Two quantitative trait loci for grain yield and plant height on chromosome 3 are tightly linked in coupling phase in rice

Abstract

Plant height is a very important trait affecting rice production. The introduction of the Green Revolution gene, sd-1, into rice cultivars to create semi-dwarfism has increased grain production. In the development of modern rice breeding, there is an urgent need for a somewhat higher plant for not only maintenance of strong lodging resistance, but also more biomass. In this study, the plant height quantitative trait locus (QTL) qPH3 with moderate effect and the yield per plant QTL qYD3 were identified on chromosome 3 in a population derived from two semi-dwarf cultivars. The 02428 alleles of both QTLs contributed to increasing phenotypic values. In the near-isogenic background, both QTLs exhibited the characteristics of a single Mendelian gene. qPH3 and qYD3 were tightly linked, no more than 130 kb apart, with additive effects of 5.2 cm and 4.4 g, respectively. They were further fine-mapped to a 19-kb region and a 65-kb region, respectively, where the recombination hotspot occurred. The gene encoding gibberellin 20-oxidase associated with plant height was regarded as the candidate of qPH3. Both linked QTLs are in coupling phase, which is convenient for simultaneously selecting both genes for breeding highyield varieties maintaining strong lodging resistance. Isolation of qYD3 is very promising due to its location in a recombination hotspot region.

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.)

“…Neighbouring QTL that are linked in coupling phase are commonly observed in primary QTL analysis (Fan et al 2017; Wu et al 2015). To date, many studies have tried to dissect QTL in coupling phase using NILs or residual heterozygous lines and found that coupling QTL were partially attributed to tightly linked independent QTL (Chemayek et al 2017; Shen et al 2011).…”

“…To date, many studies have tried to dissect QTL in coupling phase using NILs or residual heterozygous lines and found that coupling QTL were partially attributed to tightly linked independent QTL (Chemayek et al 2017; Shen et al 2011). For example, Wu et al dissected two tightly linked QTL for PHT ( qPH3 ) and yield per plant ( qYD3 ) by using two rice near isogenic populations (Wu et al 2015). In wheat, tight repulsion linkage between Sr36 and Sr39 was revealed by genetic, cytogenetic and molecular analyses (Chemayek et al 2017).…”

A Statistical Procedure for Genome-Wide Detection of QTL Hotspots Using Public Databases with Application to Rice

“…Such a procedure is easy to implement and very cheap in computation as compared to the methods by permuting the original individual-level data in the hotspot analysis (see The permutation algorithm ) . It has been observed that QTL or genes for genetically correlated traits have a tendency to cluster on the same or adjacent regions of chromosomes in several organisms, which may be due to linkage, pleiotropy or natural selection for co-adapted traits (Studer and Doebley 2011; Wu et al 2015). The grouping strategy attempts to take the clustering phenomenon into account in the detection of QTL hotspots.…”

High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus)

“…Clustering of QTLs for genetically correlated traits in the same or adjacent regions of HGs in several organisms may be due to physical linkage, pleiotropy or natural selection for coadapted traits (Studer and Doebley, 2011;Wu et al, 2015). We have taken the first step in the identification of loci that lead to these trait correlations and the degree to which these patterns affect productivity in M. maximus.…”