Mapping quantitative trait loci in tetraploid populations

Knowledge of quantitative trait locus (QTL) mapping in polyploids is almost void, albeit many exquisite strategies of QTL mapping have been proposed and extensive investigations have been carried out in diploid animals and plants. In this paper we develop a simple algorithm which uses an iteratively reweighted least square method to map QTLs in tetraploid populations. The method uses information from all markers in a linkage group to infer the probability distribution of QTL genotype under the assumption of random chromosome segregation. Unlike QTL mapping in diploid species, here we estimate and test the compound 'gametic effect', which consists of the composite 'genic effect' of alleles and higher-order gene interactions. The validity and efficiency of the proposed method are investigated through simulation studies. Results show that the method can successfully locate QTLs and separates different sources (e.g. additive and dominance) of variance components contributed by the QTLs.     

Novel quantitative trait loci for broad-based resistance to soybean cyst nematode (Heterodera glycines Ichinohe) in soybean PI 567516C

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most destructive pest of soybean worldwide. Host plant resistance is an effective approach to control this pest. Plant introduction PI 567516C has been reported to be highly resistant to multiple-HG types of SCN. The objectives of this study were to identify and map novel quantitative trait loci (QTL) for SCN resistance to six HG types (also known as races 1, 2, 3, 5, 14, and LY1). Mapping was conducted using 250 F_2:3 progeny derived from a Magellan (susceptible) × PI 567516C (resistant) cross. F_6:7 recombinant inbred lines (RILs) developed from the F_2:3 progeny were employed to confirm the putative QTL identified. A total of 927 polymorphic simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers were genotyped. Following the genetic linkage analysis, permutation tests and composite interval mapping were performed to identify and map QTL. Four QTL were associated with resistance to either multiple- or single-SCN HG types. Two QTL for resistance to multiple-SCN HG types were mapped to Chromosomes 10 and 18 and have not been reported in other SCN resistance sources. New QTL were confirmed by analysis of 250 F_6:7 RILs from the same population. SSR and SNP markers closely associated with these QTL can be useful for the development of near-isogenic lines for fine-mapping and positional cloning of candidate genes for SCN resistance.     

Integration of sudden death syndrome resistance loci in the soybean genome

Key message

Complexity and inconsistencies in resistance mapping publications of soybean sudden death syndrome (SDS) result in interpretation difficulty. This review integrates SDS mapping literature and proposes a new nomenclature system for reproducible SDS resistance loci.

Abstract

Soybean resistance to sudden death syndrome (SDS) is composed of foliar resistance to phytotoxins and root resistance to pathogen invasion. There are more than 80 quantitative trait loci (QTL) and dozens of single nucleotide polymorphisms (SNPs) associated with soybean resistance to SDS. The validity of these QTL and SNPs is questionable because of the complexity in phenotyping methodologies, the disease synergism between SDS and soybean cyst nematode (SCN), the variability from the interactions between soybean genotypes and environments, and the inconsistencies in the QTL nomenclature. This review organizes SDS mapping results and proposes the Rfv (resistance to Fusarium virguliforme) nomenclature based on supporting criteria described in the text. Among ten reproducible loci receiving our Rfv nomenclature, Rfv18-01 is mostly supported by field studies and it co-localizes to the SCN resistance locus rhg1. The possibility that Rfv18-01 is a pleiotropic resistance locus and the concern about Rfv18-01 being confounded with Rhg1 is discussed. On the other hand, Rfv06-01, Rfv06-02, Rfv09-01, Rfv13-01, and Rfv16-01 were identified both by screening soybean leaves against phytotoxic culture filtrates and by evaluating SDS severity in fields. Future phenotyping using leaf- and root-specific resistance screening methodologies may improve the precision of SDS resistance, and advanced genetic studies may further clarify the interactions among soybean genotypes, F. virguliforme, SCN, and environments. The review provides a summary of the SDS resistance literature and proposes a framework for communicating SDS resistance loci for future research considering molecular interactions and genetic breeding for soybean SDS resistance.

     

Mapping and analysis of quantitative trait loci in experimental populations

Simple statistical methods for the study of quantitative trait loci (QTL), such as analysis of variance, have given way to methods that involve several markers and high-resolution genetic maps. As a result, the mapping community has been provided with statistical and computational tools that have much greater power than ever before for studying and locating multiple and interacting QTL. Apart from their immediate practical applications, the lessons learnt from this evolution of QTL methodology might also be generally relevant to other types of functional genomics approach that are aimed at the dissection of complex phenotypes, such as microarray assessment of gene expression.     

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean

Background

Sudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of elite soybean cultivars, consisting of 392 and 300 unique accessions, respectively, were evaluated for SDS resistance in multiple environments and years. The two association panels were genotyped with 52,041 and 5,361 single nucleotide polymorphisms (SNPs), respectively. Genome-wide association mapping was carried out using a mixed linear model that accounted for population structure and cryptic relatedness.

Result

A total of 20 loci underlying SDS resistance were identified in the two independent studies, including 7 loci localized in previously mapped QTL intervals and 13 novel loci. One strong peak of association on chromosome 18, associated with all disease assessment criteria across the two panels, spanned a physical region of 1.2 Mb around a previously cloned SDS resistance gene (GmRLK18-1) in locus Rfs2. An additional variant independently associated with SDS resistance was also found in this genomic region. Other peaks were within, or close to, sequences annotated as homologous to genes previously shown to be involved in plant disease resistance. The identified loci explained an average of 54.5% of the phenotypic variance measured by different disease assessment criteria.

Conclusions

This study identified multiple novel loci and refined the map locations of known loci related to SDS resistance. These insights into the genetic basis of SDS resistance can now be used to further enhance durable resistance to SDS in soybean. Additionally, the associations identified here provide a basis for further efforts to pinpoint causal variants and to clarify how the implicated genes affect SDS resistance in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-809) contains supplementary material, which is available to authorized users.     

Confirmation of two quantitative trait loci regions for nematode resistance in commercial British terminal sire breeds

Sheep internal parasites (nematodes) remain a major health challenge and are costly for pasture-based production systems. Most current breeding programmes for nematode resistance are based on indicator traits such as faecal egg counts (FEC), which are costly and laborious to collect. Hence, genetic markers for resistance would be advantageous. However, although some quantitative trait loci (QTL) have been identified, these QTL are often not consistent across breeds and few breeding strategies for nematode resistance in sheep are currently using molecular information. In this study, QTL for nematode resistance on ovine chromosomes (OAR) 3 and 14, previously identified in the Blackface breed, were explored using commercial Suffolk (n = 336) and Texel lambs (n = 879) sampled from terminal sire breeder flocks in the United Kingdom. FEC were used as the indicator trait for nematode resistance, and these were counted separately for Nematodirus and Strongyles genera. Microsatellite markers were used to map the QTL and the data were analysed using interval mapping regression techniques and variance component analysis. QTL for Nematodirus and Strongyles FEC were found to be segregating on OAR3 at 5% chromosome region-wide significance threshold in both Suffolk and Texel sheep, and Nematodirus FEC QTL were segregating on OAR14 in both breeds. In addition, QTL for growth traits were also found to be segregating at 5% chromosome region-wide on OAR3 and OAR14. The confirmation that FEC QTL segregate in the same position in three widely used breeds widens their potential applicability to purebred Blackface, Suffolk and Texel sheep, with benefits likely to be observed in their commercial crossbred progeny.     

Mapping quantitative trait loci for preharvest sprouting resistance in white wheat

The premature germination of seeds before harvest, known as preharvest sprouting (PHS), is a serious problem in all wheat growing regions of the world. In order to determine genetic control of PHS resistance in white wheat from the relatively uncharacterized North American germplasm, a doubled haploid population consisting of 209 lines from a cross between the PHS resistant variety Cayuga and the PHS susceptible variety Caledonia was used for QTL mapping. A total of 16 environments were used to detect 15 different PHS QTL including a major QTL, QPhs.cnl-2B.1, that was significant in all environments tested and explained from 5 to 31% of the trait variation in a given environment. Three other QTL QPhs.cnl-2D.1, QPhs.cnl-3D.1, and QPhs.cnl-6D.1 were detected in six, four, and ten environments, respectively. The potentially related traits of heading date (HD), plant height (HT), seed dormancy (DOR), and rate of germination (ROG) were also recorded in a limited number of environments. HD was found to be significantly negatively correlated with PHS score in most environments, likely due to a major HD QTL, QHd.cnl-2B.1, found to be tightly linked to the PHS QTL QPhs.cnl-2B.1. Using greenhouse grown material no overlap was found between seed dormancy and the four most consistent PHS QTL, suggesting that greenhouse environments are not representative of field environments. This study provides valuable information for marker-assisted breeding for PHS resistance, future haplotyping studies, and research into seed dormancy.     

Mapping quantitative trait loci for downy mildew resistance in pearl millet

Quantitative trait loci (QTLs) for resistance to pathogen populations of Scelerospora graminicola from India, Nigeria, Niger and Senegal were mapped using a resistant x susceptible pearl millet cross. An RFLP map constructed using F₂ plants was used to map QTLs for traits scored on F₄ families. QTL analysis was carried out using the interval mapping programme Mapmaker/QTL. Independent inheritance of resistance to pathogen populations from India, Senegal, and populations from Niger and Nigeria was shown. These results demonstrate the existence of differing virulences in the pathogen populations from within Africa and between Africa and India. QTLs of large effect, contributing towards a large porportion of the variation in resistance, were consistently detected in repeated screens. QTLs of smaller and more variable effect were also detected. There was no QTLs that were effective against all four pathogen populations, demonstrating that pathotype-specific resistance is a major mechanism of downy mildew resistance in this cross. For all but one of the QTLs, resistance was inherited from the resistant parent and the inheritance of resistance tended to be the result of dominance or over-dominance. The implications of this research for pearl millet breeding are discussed.     

Mapping quantitative trait loci associated with barley net blotch resistance

Net blotch of barley, caused by Pyrenophora teres Drechs., is an important foliar disease worldwide. Deployment of resistant cultivars is the most economic and eco-friendly control method. This report describes mapping of quantitative trait loci (QTL) associated with net blotch resistance in a doubled-haploid (DH) barley population using diversity arrays technology (DArT) markers. One hundred and fifty DH lines from the cross CDC Dolly (susceptible)/TR251 (resistant) were screened as seedlings in controlled environments with net-form net blotch (NFNB) isolates WRS858 and WRS1607 and spot-form net blotch (SFNB) isolate WRS857. The population was also screened at the adult-plant stage for NFNB resistance in the field in 2005 and 2006. A high-density genetic linkage map of 90 DH lines was constructed using 457 DArT and 11 SSR markers. A major NFNB seedling resistance QTL, designated QRpt6, was mapped to chromosome 6H for isolates WRS858 and WRS1607. QRpt6 was associated with adult-plant resistance in the 2005 and 2006 field trials. Additional QTL for NFNB seedling resistance to the more virulent isolate WRS858 were identified on chromosomes 2H, 4H, and 5H. A seedling resistance QTL (QRpts4) for the SFNB isolate WRS857 was detected on chromosome 4H as was a significant QTL (QRpt7) on chromosome 7H. Three QTL (QRpt6, QRpts4, QRpt7) were associated with resistance to both net blotch forms and lines with one or more of these demonstrated improved resistance. Simple sequence repeat (SSR) markers tightly linked to QRpt6 and QRpts4 were identified and validated in an unrelated barley population. The major 6H QTL, QRpt6, may provide adequate NFNB field resistance in western Canada and could be routinely selected for using molecular markers in a practical breeding program.     

Mapping of quantitative trait loci for canopy-wilting trait in soybean (Glycine max L. Merr)

Drought stress adversely affects [Glycine max (L.) Merr] soybean at most developmental stages, which collectively results in yield reduction. Little information is available on relative contribution and chromosomal locations of quantitative trait loci (QTL) conditioning drought tolerance in soybean. A Japanese germplasm accession, PI 416937, was found to possess drought resistance. Under moisture-deficit conditions, PI 416937 wilted more slowly in the field than elite cultivars and has been used as a parent in breeding programs to improve soybean productivity. A recombinant inbred line (RIL) population was derived from a cross between PI 416937 and Benning, and the population was phenotyped for canopy wilting under rain-fed field conditions in five distinct environments to identify the QTL associated with the canopy-wilting trait. In a combined analysis over environments, seven QTL that explained 75?% of the variation in canopy-wilting trait were identified on different chromosomes, implying the complexity of this trait. Five QTL inherited their positive alleles from PI 416937. Surprisingly, the other two QTL inherited their positive alleles from Benning. These putative QTL were co-localized with other QTL previously identified as related to plant abiotic stresses in soybean, suggesting that canopy-wilting QTL may be associated with additional morpho-physiological traits in soybean. A locus on chromosome 12 (Gm12) from PI 416937 was detected in the combined analysis as well as in each individual environment, and explained 27?% of the variation in canopy-wilting. QTL identified in PI 416937 could provide an efficient means to augment field-oriented development of drought-tolerant soybean cultivars.     

Genetic mapping of soybean cyst nematode race-3 resistance loci in the soybean PI 437.654

Resistance to the soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is difficult to evaluate in soybean [Glycine max (L.) Merr.] breeding. PI 437.654 has resistance to more SCN race isolates than any other known soybean. We screened 298 F₆₇ recombinant-inbred lines from a cross between PI 437.654 and BSR101 for SCN race-3 resistance, genetically mapped 355 RFLP markers and the I locus, and tested these markers for association with resistance loci. The Rhg ₄ resistance locus was within 1 cM of the I locus on linkage group A. Two additional QTLs associated with SCN resistance were located within 3cM of markers on groups G and M. These two loci were not independent because 91 of 96 lines that had a resistant-parent marker type on group G also had a resistant-parent marker type on group M. Rhg ₄ and the QTL on G showed a significant interaction by together providing complete resistance to SCN race-3. Individually, the QTL on G had greater effect on resistance than did Rhg ₄, but neither locus alone provided a degree of resistance much different from the susceptible parent. The nearest markers to the mapped QTLs on groups A and G had allele frequencies from the resistant parent indicating 52 resistant lines in this population, a number not significantly different from the 55 resistant lines found. Therefore, no QTLs from PI 437.654 other than those mapped here are expected to be required for resistance to SCN race-3. All 50 lines that had the PI 437.654 marker type at the nearest marker to each of the QTLs on groups A and G were resistant to SCN race-3. We believe markers near to these QTLs can be used effectively to select for SCN race-3 resistance, thereby improving the ability to breed SCN-resistant soybean varieties.     

Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome

Soybean [Glycine max (L.) Merr.] cultivars show differences in their resistance to both the leaf scorch and root rot of sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Root susceptibility combined with reduced leaf scorch resistance has been associated with resistance to Heterodera glycines HG Type 1.3.6.7 (race 14) of the soybean cyst nematode (SCN). In contrast, the rhg1 locus underlying resistance to Hg Type 0 was found clustered with three loci for resistance to SDS leaf scorch and one for root infection. The aims of this study were to compare the inheritance of resistance to leaf scorch and root infection in a population that segregated for resistance to SCN and to identify the underlying quantitative trait loci (QTL). “Hartwig”, a cultivar partially resistant to SDS leaf scorch, F. virguliforme root infection and SCN HG Type 1.3.6.7 was crossed with the partially susceptible cultivar “Flyer”. Ninety-two F5-derived recombinant inbred lines and 144 markers were used for map development. Four QTL found in earlier studies were confirmed. One contributed resistance to leaf scorch on linkage group (LG) C2 (Satt277; P = 0.004, R ² = 15%). Two on LG G underlay root infection at R8 (Satt038; P = 0.0001 R ² = 28.1%; Satt115; P = 0.003, R ² = 12.9%). The marker Satt038 was linked to rhg1 underlying resistance to SCN Hg Type 0. The fourth QTL was on LG D2 underlying resistance to root infection at R6 (Satt574; P = 0.001, R ² = 10%). That QTL was in an interval previously associated with resistance to both SDS leaf scorch and SCN Hg Type 1.3.6.7. The QTL showed repulsion linkage with resistance to SCN that may explain the relative susceptibility to SDS of some SCN resistant cultivars. One additional QTL was discovered on LG G underlying resistance to SDS leaf scorch measured by disease index (Satt130; P = 0.003, R ² = 13%). The loci and markers will provide tagged alleles with which to improve the breeding of cultivars combining resistances to SDS leaf scorch, root infection and SCN HG Type 1.3.6.7. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Detection of quantitative trait loci for resistance to gastrointestinal nematode infections in Creole goats

This study aimed to identify regions of the genome affecting resistance to gastrointestinal nematodes in a Creole goat population naturally exposed to a mixed nematode infection (Haemonchus contortus, Trichostrongylus colubriformis and Oesophagostomum columbianum) by grazing on irrigated pasture. A genome‐wide quantitative trait loci (QTL) scan was performed on 383 offspring from 12 half‐sib families. A total of 101 microsatellite markers were genotyped. Traits analysed were faecal egg count (FEC), packed cell volume (PCV), eosinophil count and bodyweight (BW) at 7 and 11 months of age. Levels of activity of immunoglobulin A (IgA) and activity of immunoglobulin E (IgE) anti‐Haemonchus contortus L3 crude extracts and adult excretion/secretion products (ESPs) were also analysed. Using interval mapping, this study identified 13 QTL for parasite resistance. Two QTL linked with FEC were found on chromosomes 22 and 26. Three QTL were detected on chromosomes 7, 8 and 14 for eosinophil counts. Three QTL linked with PCV were identified on chromosomes 5, 9 and 21. A QTL for BW at 7 months of age was found on chromosome 6. Lastly, two QTL detected on chromosomes 3 and 10 were associated with IgE anti‐L3, and IgE anti‐ESP was linked with two QTL on chromosomes 1 and 26. This study is the first to have identified regions of the genome linked with nematode resistance in a goat population using a genome scan. These results provide useful tools for the understanding of parasite resistance in small ruminants.     

Mapping quantitative trait loci in oligogenic models

We discuss strategies for mapping quantitative trait loci with emphasis on certain issues of study design that have recently received attention: e.g. genotyping only selected pedigrees and the comparative value of large pedigrees versus sib pairs. We use a standard variance components model and a parametrization of the genetic effects in which the 'segregation' parameters are locally orthogonal to the 'linkage' parameters. This permits simple explicit expressions for the expectation of the score statistic, which we use to compare the power of different strategies. We also discuss robustness of the score statistic.     

Mapping quantitative trait loci using the experimental designs of recombinant inbred populations

In the data collection of the QTL experiments using recombinant inbred (RI) populations, when individuals are genotyped for markers in a population, the trait values (phenotypes) can be obtained from the genotyped individuals (from the same population) or from some progeny of the genotyped individuals (from the different populations). Let Fu be the genotyped population and Fv (v>or=u) be the phenotyped population. The experimental designs that both marker genotypes and phenotypes are recorded on the same populations can be denoted as (Fu/Fv, u=v) designs and that genotypes and phenotypes are obtained from the different populations can be denoted as (Fu/Fv, v>u) designs. Although most of the QTL mapping experiments have been conducted on the backcross and F2(F2/F2) designs, the other (Fu/Fv, v>or=u) designs are also very popular. The great benefits of using the other (Fu/Fv, v>or=u) designs in QTL mapping include reducing cost and environmental variance by phenotyping several progeny for the genotyped individuals and taking advantages of the changes in population structures of other RI populations. Current QTL mapping methods including those for the (Fu/Fv, u=v) designs, mostly for the backcross or F2/F2 design, and for the F2/F3 design based on a one-QTL model are inadequate for the investigation of the mapping properties in the (Fu/Fv, uor=u) designs. In addition, the QTL mapping properties of the proposed and approximate methods in different designs are discussed. Simulations were performed to evaluate the performance of the proposed and approximate methods. The proposed method is proven to be able to correct the problems of the approximate and current methods for improving the resolution of genetic architecture of quantitative traits and can serve as an effective tool to explore the QTL mapping study in the system of RI populations.     

Mapping quantitative trait loci for bovine ovulation rate

An elite, three-generation family from the USDA Meat Animal Research Center twinning population was examined for evidence of ovulation rate quantitative trait loci (QTL). This work was both a continuation of previously reported results suggesting evidence for ovulation rate QTL on bovine Chromosome (Chr) 7 and an extension of a genome-wide search for QTL. Additional markers were typed on Chr 7 to facilitate interval mapping and testing of the hypothesis of one versus two QTL on that chromosome. In addition, 14 other informative markers were added to a selective genotyping genome screening of this family, and markers exhibiting nominal significance were used to identify chromosomal regions that were then subjected to more exhaustive analysis. For Chr 7, a total of 12 markers were typed over a region spanning the proximal two-thirds of the chromosome. Results from interval mapping analyses indicated evidence suggestive of the presence of QTL (nominal P < 0.00077) within this region. Subsequent analysis with a model postulating two QTL provided evidence (P < 0.05) for two rather than one QTL on this chromosome. Preliminary analysis with additional markers indicated nominal significance (P < 0.05) for regions of Chrs 5, 10, and 19. Each of these regions was then typed with additional markers for the entire three-generation pedigree. Significant evidence (P < 0.000026) of ovulation rate QTL was found for Chrs 5 and 19, while support on Chr 10 failed to exceed a suggestive linkage threshold (P > 0.00077). Received: 14 May 1999 / Accepted: 14 October 1999     

Mapping and quantitative trait loci analysis of verticillium wilt resistance genes in cotton

Verticillium wilt is one of the most serious constraints to cotton production in almost all of the cotton-growing countries. In this study, ＂XinLuZaol＂ （XLZl）, a susceptible cultivar Gossypium hirsutum L. and ＂Hai7124＂ （H7124）, a resistant line G. barbadense, and their F2：3 families were used to map and study the disease index induced by verticillium wilt. A total of 430 SSR loci were mapped into 41 linkage groups; the map spanned 3 745.9 cM and the average distance between adjacent loci was 8.71 cM. Four and five quantitative trait loci （QTLs） were detected based on the disease index investigated on July 22 and August 24 in 2004, respectively. These nine QTLs explained 10.63-28.83% of the phenotypic variance, six of them were located on the D sub-genome. Two QTLs located in the same marker intervals may partly explain the significant correlation of the two traits. QTLs explaining large phenotypic variation were identified in this study, which may be quite useful in cotton anti-disease breeding.     

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

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.