Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach

Abstract

Quantitative trait locus (QTL) mapping is often conducted in line-crossing experiments where a sample of individuals is randomly selected from a pool of all potential progeny. QTLs detected from such an experiment are important for us to understand the genetic mechanisms governing a complex trait, but may not be directly relevant to plant breeding if they are not detected from the breeding population where selection is targeting for. QTLs segregating in one population may not necessarily segregate in another population. To facilitate marker-assisted selection, QTLs must be detected from the very population which the selection is targeting. However, selected breeding populations often have depleted genetic variation with small population sizes, resulting in low power in detecting useful QTLs. On the other hand, if selection is effective, loci controlling the selected trait will deviate from the expected Mendelian segregation ratio. In this study, we proposed to detect QTLs in selected breeding populations via the detection of marker segregation distortion in either a single population or multiple populations using the same selection scheme. Simulation studies showed that QTL can be detected in strong selected populations with selected population sizes as small as 25 plants. We applied the new method to detect QTLs in two breeding populations of rice selected for high grain yield. Seven QTLs were identified, four of which have been validated in advanced generations in a follow-up study. Cloned genes in the vicinity of the four QTLs were also reported in the literatures. This mapping-by-selection approach provides a new avenue for breeders to improve breeding progress. The new method can be applied to breeding programs not only in rice but also in other agricultural species including crops, trees and animals. Heredity (2015) 115, 538-546; doi:10.1038/hdy.2015.56; published online 1 July 2015 INTRODUCTIONOver a century of breeding efforts has produced numerous varieties of domestic plants and animals to provide ample food resources for human. The great successes in plant and animal breeding have largely been achieved by exploiting within-species genetic variation for traits of interest through phenotypic selection. Although appropriate phenotypic selection is effective to exploit useful genetic variation of complex traits in breeding populations, the rich sources of naturally occurring genetic variation in plants and animals are largely hidden at the phenotypic levels and remain uncharacterized at the genomic and molecular levels. As a result, they are very much under-utilized in the past breeding programs. Meanwhile, the past decades have witnessed tremendous progress in genetic dissections of complex traits in plants and animals using DNA markers and genomic technologies (Francia et al., 2005;Collard and Mackill, 2008;Miah et al., 2013). During this period of time, thousands of quantitative trait locus (QTL) affecting a wide range of complex traits have been identified in different plant and animal species. These ...

QTLs identified for Biofortification Traits in Wheat: A Review

“…Conventional breeding methods are easy to operate with qualitative traits. These traits depend on a single gene whereas traits like yield are quantitative and therefore are impacted by several genes [27,28,29]. There are several techniques for mapping quantitative trait loci (QTL) in an experimental cross [30].…”

Генетичний та асоціативний аналіз однонуклеотидного поліморфізму g.22 G>C у гені катепсину F свиней різних порід

“…Встановлено велику кількість генівкандидатів, що належать до таких локусів (локуси кількісних ознак, QTL -quantitative traits loci), які впливають на репродуктивні, відгодівельні і м'ясні якості свиней. Але серед них відомо не так багато генів і відповідних ДНК маркерів, які з точки зору їх інформативності і сили асоціації з ознаками, можна ефективно використовувати у практиці селекційної роботи [2,11].…”

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

“…Linkage maps constructed with segregation-distorted markers have been applied in identifying candidate genes or regions relevant to important agronomic traits (Cui et al, 2015;Xu and Hu, 2009;Zhang et al, 2010). To assess the efficiency of QTL mapping with segregation-distorted markers in our analysis, 14 agronomic traits (12 quantitative traits and 2 qualitative traits) were measured for 152 randomly selected RILs.…”

“…Chromosomes with only a few segregationdistorted loci can cause large chromosome segments or entire chromosome to be deviated from Mendelian segregation (Xu, 2008). Moreover, segregation-distorted markers are presumed to be related to QTLs controlling certain traits in selected populations (Cui et al, 2015). Using segregation-distorted markers leads to higher genetic variance and better identification of QTL than using non-distorted markers (Hackett and Broadfoot, 2003;Zhang et al, 2010).…”

“…However, segregation-distorted markers are usually discarded when building linkage maps and mapping QTLs, resulting in low marker density and failure in identifying biologically interesting segments (Xu and Hu, 2009). Several efficient and powerful programs have been proposed to allow researchers to overcome these problems and include segregation-distorted markers in analysis (Cui et al, 2015;Lorieux, 2012;Shah et al, 2014;Xu, 2008).…”