Putative Quantitative Trait Loci Regions Research Articles

Deciphering the genetic architecture of β-glucan content in oats (Avena sativa L.) through QTL mapping

Oat is a cereal grain grown for human and animal nutrition. It is known for its high dietary fibre content, phytochemicals, and nutritional value. The primary component of oat fibre is β-glucan, a group of polysaccharides comprising mixed-linkage (1,3) (1,4)-D-glucose units. The β-glucan concentrations of oat cultivars usually range from 3 to 6% and are considered a polygenic trait controlled by multiple genes with additive effects. The primary goal of this study was to identify quantitative trait loci (QTLs) for β-glucan content. Two contrasting parents for β-glucan content, OL10 (5.8%) and OL11 (0.8%), were selected from 91 germplasm lines, and an F2:4 mapping population was generated for QTL mapping. Five genotypes with the highest levels of β-glucan content were observed. The QTLs affecting β-glucan content were identified using QTL cartographer, employing single marker analysis (SMA) and composite interval mapping (CIM). Two putative QTL regions were identified, one on linkage group (LG) 1 and the other on LG 4, with LOD (logarithm of the odds) scores of 3.7 and 4.3, respectively, explaining 31 and 33% of the phenotypic variation. The information generated is important in identifying the genomic regions responsible for β-glucan content in oats.

Identification and analysis of genes causing varietal differences of cesium accumulation in soybean

ABSTRACT Here, we explored the genomic loci and genes responsible for differences in Cs accumulation in the seeds of two soybean (Glycine max (L.) Merr.) cultivars, namely ‘Enrei’ (high accumulator) and ‘Onihadaka’ (low accumulator), using quantitative trait loci (QTL)-seq. For analysis, F3 and F5 generations were generated by crossing the two cultivars followed by self-fertilization. In the putative QTL regions of the F3 generation, Glyma.11G099100 annotated as the vacuolar sorting protein/ubiquitin receptor VPS23 was found. VPS23A regulates the salt overly sensitive (SOS) signaling cascade in Arabidopsis, and mutations in SOS2 reduce radiocesium accumulation in rice grains. In the putative QTL regions of the F5 generation, Glyma.06G112200, which is a homolog of the usually multiple acids move in and out transporter (UMAMIT) proteins in Arabidopsis, was found. UMAMIT proteins are the exporters of amino acids, and the addition of cysteine or its derivative methyl cysteine to the growth medium increased Cs accumulation in A. thaliana. Both Glyma.11G099100 and Glyma.06G112200 carried polymorphisms – an amino acid substitution – between ‘Enrei’ and ‘Onihadaka.’ Yeast cells heterologously expressing the Onihadaka-type Glyma.06G112200 showed higher Cs accumulation than those expressing the Enrei-type. Yeast cells expressing the Enrei-type Glyma.06G112200 showed lower Cs accumulation than the vector controls; however, there was no significant difference between yeast cells expressing the Onihadaka-type and the vector controls. These results suggest that variations in the sequences of Glyma.11G099100 and Glyma.06G112200 in ‘Enrei’ and ‘Onihadaka’ are possibly responsible for differences in Cs uptake between these soybean cultivars.

Genetic correlation and genome-wide association study (GWAS) of the length of productive life, days open, and 305-days milk yield in crossbred Holstein dairy cattle.

In this study, we estimated the genetic parameters and identified the putative quantitative trait loci (QTL) associated with the length of productive life (LPL), days open (DO), and 305-day milk yield for the first lactation (FM305) of crossbred Holstein dairy cattle. Data comprising 4,739 records collected between 1986 and 2004 were used to estimate the variance-covariance components using the multiple-trait animal linear mixed models based on the average information restricted maximum likelihood (AI-REML) algorithm. Thirty-six animals were genotyped using the Illumina BovineSNP50 Bead Chip [>50,000 single nucleotide polymorphisms (SNPs)] to identify the putative QTL in a genome-wide association study. The heritability of the production trait FM305 was 0.25 and that of the functional traits, LPL and DO, was low (0.10 and 0.06, respectively). The genetic correlation estimates demonstrated favorable negative correlations between LPL and DO (-0.02). However, we observed a favorable positive correlation between FM305 and LPL (0.43) and an unfavorable positive correlation between FM305 and DO (0.1). The GWAS results indicated that 23 QTLs on bovine chromosomes 1, 4, 5, 8, 15, 26, and X were associated with the traits of interest, and the putative QTL regions were identified within seven genes (SYT1, DOCK11, KLHL13, IL13RA1, PRKG1, GNA14, and LRRC4C). In conclusion, the heritability estimates of the LPL and DO were low. Therefore, the approach of multiple-trait selection indexes should be applied, and the QTL identified here should be considered for use in marker-assisted selection in the future.

Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits.

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

Identification of Candidate Genes Associated with Beef Marbling Using QTL and Pathway Analysis in Hanwoo (Korean Cattle).

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

A genome‐wide association study for quantitative trait loci of show‐jumping in Hanoverian warmblood horses

Show-jumping is an economically important breeding goal in Hanoverian warmblood horses. The aim of this study was a genome-wide association study (GWAS) for quantitative trait loci (QTL) for show-jumping in Hanoverian warmblood horses, employing the Illumina equine SNP50 Beadchip. For our analyses, we genotyped 115 stallions of the National State stud of Lower Saxony. The show-jumping talent of a horse includes style and ability in free-jumping. To control spurious associations based on population stratification, two different mixed linear animal model (MLM) approaches were employed, besides linear models with fixed effects only and adaptive permutations for correcting multiple testing. Population stratification was explained best in the MLM considering Hanoverian, Thoroughbred, Trakehner and Holsteiner genes and the marker identity-by-state relationship matrix. We identified six QTL for show-jumping on horse chromosomes (ECA) 1, 8, 9 and 26 (-log(10) P-value >5) and further putative QTL with -log(10) P-values of 3-5 on ECA1, 3, 11, 17 and 21. Within six QTL regions, we identified human performance-related genes including PAPSS2 on ECA1, MYL2 on ECA8, TRHR on ECA9 and GABPA on ECA26 and within the putative QTL regions NRAP on ECA1, and TBX4 on ECA11. The results of our GWAS suggest that genes involved in muscle structure, development and metabolism are crucial for elite show-jumping performance. Further studies are required to validate these QTL in larger data sets and further horse populations.

Correlation between per se and Testcross Performance in Rye (Secale cereale L.) Introgression Lines Estimated with a Bivariate Mixed Linear Model

ABSTRACTIn hybrid breeding a high correlation between per se performance of parental lines and hybrid performance can help to reduce the efforts for testcross trials. Our objectives were (i) to investigate the correlation between per se and testcross performance of rye (Secale cereale L.) candidate introgression lines (pre‐ILs) for thousand‐kernel weight, test weight, falling number, starch, pentosan, and protein content; and (ii) to investigate the consistency of quantitative trait loci (QTL) determined in pre‐ILs and their testcross progenies. Eighty pre‐ILs carrying donor chromosome segments (DCS) from the Iranian primitive rye Altevogt 14160 in the genetic background of elite line L2053‐N, were evaluated at four locations over 2 yr. Genetic correlations between per se and testcross performance were estimated with a bivariate mixed linear model. Putative QTL regions were detected by comparing the performance of pre‐ILs carrying certain DCS with the performance of the recurrent parent. Genotypic variances and heritabilities were higher for per se than for testcross performance. Genetic correlations between per se and testcross performance were mostly intermediate. Common QTL regions were observed for test weight, starch, pentosan, and protein content. Our results revealed that a superior per se performance of rye pre‐ILs is not indicative for a superior hybrid performance. Consequently, using rye pre‐ILs in hybrid breeding programs requires testcross trials.

QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus)

The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.

Mapping quantitative trait loci for osteochondrosis in fetlock and hock joints and palmar/plantar osseus fragments in fetlock joints of South German Coldblood horses

The aim of this study was to identify quantitative trait loci (QTL) for osteochondrosis (OC) and palmar/plantar osseous fragments (POF) in fetlock joints in a whole-genome scan of 219 South German Coldblood horses. Symptoms of OC and POF were checked by radiography in 117 South German Coldblood horses at a mean age of 17 months. The radiographic examination comprised the fetlock and hock joints of all limbs. The genome scan included 157 polymorphic microsatellite markers. All microsatellite markers were equally spaced over the 31 autosomes and the X chromosome, with an average distance of 17.7 cM and a mean polymorphism information content (PIC) of 63%. Sixteen chromosomes harbouring putative QTL regions were further investigated by genotyping the animals with 93 additional markers. QTL that had chromosome-wide significance by non-parametric Z-means and LOD scores were found on 10 chromosomes. This included seven QTL for fetlock OC and one QTL on ECA18 associated with hock OC and fetlock OC. Significant QTL for POF in fetlock joints were located on equine chromosomes 1, 4, 8, 12 and 18. This genome scan is an important step towards the identification of genes responsible for OC in horses.

Genetic mapping of hop (Humulus lupulusL.) applied to the detection of QTLs for alpha-acid content

The map locations and effects of quantitative trait loci (QTLs) were estimated for alpha-acid content in hop (Humulus lupulus L.) using amplified fragment length polymorphism (AFLP) and microsatellite marker (simple sequence repeat (SSR)) genetic linkage maps constructed from a double pseudotestcross. The mapping population consisted of 111 progeny from a cross between the German hop cultivar 'Magnum', which exhibits high levels of alpha-acids, and a wild Slovene male hop, 2/1. The progeny segregated quantitatively for alpha-acid content determined in 2002, 2003, and 2004. The maternal map consisted of 96 markers mapped on 14 linkage groups defining 661.90 cM of total map distance. The paternal map included 70 markers assigned to 12 linkage groups covering 445.90 cM of hop genome. QTL analysis indicated 4 putative QTLs (alpha1, alpha2, alpha3, and alpha4) on linkage groups (LGs) 03, 01, 09, and 03 of the female map, respectively. QTLs explained 11.9%-24.8% of the phenotypic variance. The most promising QTL to be used in marker-assisted selection is alpha2, the peak of which colocated exactly with the AFLP marker. Three chalcone synthase-like genes (chs2, chs3, and chs4) involved in hop bitter acid synthesis mapped together on LG04 of the female map. Saturation of the maps, particularly the putative QTL regions, will be carried out using SSR markers, and the stability of the QTLs will be tested in the coming years.

QTL mapping for resistance against the European corn borer (Ostrinia nubilalis H.) in early maturing European dent germplasm

The European corn borer (ECB, Ostrinia nubilalis Hubner) is a major pest of maize in Central Europe. We mapped and characterized quantitative trait loci (QTLs) involved in resistance of maize against ECB damage, compared them with QTLs for agronomic traits, and evaluated the usefulness of marker-assisted selection (MAS) for improving ECB resistance in early maturing European maize germplasm. A total 226 F3 families from the cross D06 (resistant) × D408 (susceptible), together with 93 RFLP and two SSR markers were used for the QTL analyses. For each F3 family we measured the length of tunnels produced by larval stalk mining (TL), stalk damage ratings (SDR), and relative grain yield (RGY) in field experiments, with two replications in two environments in 1 year. The agronomic traits comprised grain yield under insecticide protection (GYP) and manual ECB larval infestation (GYI), the date of anthesis (ANT), and the in vitro digestibility of organic matter (IVDOM) of stover. Estimates of genotypic variance (σ2 g) were highly significant for all traits. Six QTLs for TL and five QTLs for SDR were detected, explaining about 50.0% of σ2 g. Most QTLs showed additive gene action for TL and dominance for SDR. No QTL was found for RGY. The number of QTLs detected for the agronomic traits ranged from two for GYI to 12 for ANT, explaining 12.5 to 57.3% of σ2 g, respectively. Only a single QTL was in common between the two resistance traits, as expected from the moderate trait correlation and the moderate proportions of σ2 g explained. Based on these results, MAS for improving ECB resistance can be competitive when cost-effective PCR-based marker systems are applied. However, it remains to be established whether the putative QTL regions for ECB resistance detected in the population D06 × D408 are consistent across other early maturing European maize germplasms.