Seed dormancy is an important trait associated with pre-sprouting and malting quality in barley. Genome-wide association studies (GWASs) have been used to detect quantitative trait loci (QTLs) underlying complex traits in major crops. In the present study, we collected 295 barley (Hordeum vulgare L.) accessions from Australia, Europe, Canada and China. A total of 25,179 single nucleotide polymorphism (SNP)/diversity arrays technology sequence markers were used for population structure, linkage disequilibrium and GWAS analysis. Candidate genes within QTL regions were investigated, and their expression levels were analysed using RNAseq data. Five QTLs for seed dormancy were identified. One QTL was mapped on chromosome 1H, and one QTL was mapped on chromosome 4H, while three QTLs were located on chromosome 5H. This is the first report of a QTL on the short arm of chromosome 5H in barley. Molecular markers linked to the QTL can be used for marker-assisted selection in barley breeding programmes.

Peanut (Arachis hypogaea L.) is an important row crop rich in oil, protein, vitamins and other micro-nutrients. The intensive selection of the cultigen, a cultivated plant deliberately altered by humans through cultivation, has resulted in favourable changes in yield and biochemical composition. Nevertheless, it has generated a narrow genetic basis that limits the development of new varieties with resistance to pests, diseases and environmental stresses. In this study, we address this limitation by characterizing the proximate and fatty acid composition of a multi-disease-resistant interspecific recombinant inbred line (RIL) population derived from three wild Arachis species and a cultivated elite peanut line that is being used to widen the genetic basis of the crop. The population was also genotyped with the Axiom Arachis 48K SNP array and used to detect quantitative trait loci (QTL) for oil, protein content and oleic and linoleic fatty acid percentages. A wide range of proximate composition was found in the RIL population. Eighteen and 11 individuals had high oil and protein content, respectively, and no undesirable traits related to oil quality had been introduced into the population from wild species. The fatty acid composition of oleic and linoleic acids was found to be regulated by two major QTL. The discovery of markers within the major effect QTL for the most significant chemical traits provides new opportunities for the creation of resistant and extremely nutrient-dense peanut cultivars.

Fine mapping and discovery of watermelon rind trait candidate genes are of great significance for modern watermelon breeding and development. In this study, we used the high-resolution genetic mapping and genome-wide genetic variation detection technology, combined with genome survey and sequencing technology, to locate and discover the candidate genes for rind traits of star watermelon varieties ‘Su XuanBai’ and ‘SHLX21’. Firstly, we identified a total of eight quantitative trait loci (QTLs) related to watermelon rind traits on chromosome 6. Secondly, a total of 208,240 single nucleotide polymorphisms and 75,345 small Indels (insertions/deletions) were detected in the two parents by high-coverage re-sequencing, respectively. Based on the genetic variation of the two parents and combined with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using the planta database, the QTL region was reduced to 0.02 Mb. Finally, we identified the six potential regulatory factors for watermelon rind traits using real-time quantitative PCR. In conclusion, our results revealed the fine localization of candidate genes for watermelon rind traits and the successful discovery of candidate genes for regulating watermelon rind traits, which is of importance for watermelon rind traits and breeding-improved watermelon varieties.

The aim was to study the effect of the threshold number on the accuracy of genomic evaluation of the threshold traits using support vector machine (SVM), genomic best linear unbiased prediction (GBLUP) and Bayesian method B (BayesB). For this purpose, a genome consisting of three chromosomes was simulated for 1000 individuals on which 3000 bi-allelic single nucleotide polymorphism markers were evenly distributed. Genomic breeding values were predicted in different scenarios of threshold number (1–6 thresholds), QTL number (30 and 300 QTLs) and heritability level (0.1, 0.3 and 0.5). By increasing the number of thresholds from 1 to 6 thresholds, especially at higher levels of heritability, the accuracy of genomic evaluation increased; however, the increase in accuracy was not linear so that it was much more noticeable when the number of thresholds increased from 1 to 2 thresholds. In the most studied scenarios, SVM showed a very poor performance compared to other methods. BayesB ranked first regarding prediction accuracy, though in some cases the observed differences with GBLUP was not significant. While increase in heritability increased the accuracy of genomic evaluation, change in the QTL number had a slight effect on the prediction accuracy. According to the results, the SVM is not recommended for genomic evaluation of threshold traits, especially those which have only one threshold and instead, use of GBLUP and BayesB is recommended. For traits with more than one threshold, fortunately we can achieve accuracy similar to continuous traits by applying traditional genomic evaluation methods.

Chromosome substitution strains (also called consomic lines or strains) are strains in which a single, full-length chromosome from one inbred strain — the donor strain — has been transferred onto the genetic background of a second inbred strain — the host strain. Based on the results obtained from behavioural tests with the two parental strains, the minimum number of animals from each of the host and consomic strains that are required for a successful behavioural genetic analysis can be estimated. Correct application of statistical knowledge can lead to a further reduction in the number of animals used in behavioural genetic experiments using chromosome substitution strains.

Drought is a major concern among abiotic stresses in wheat (Triticum aestivum L.) production. Breeding resistant cultivars are the most effective means to manage drought stress. F6 recombinant inbred lines (RIL) derived from the cross of Berkut/Worrakatta were used to identify quantitative trait loci (QTL) for drought tolerance at germination stage under treatment of PEG6000 using the wheat 50 K single nucleotide polymorphism (SNP) array. Twenty-eight linkage groups were constructed, covering a length of 2220.26 cM. Eighteen QTL were detected based on the drought tolerance coefficients and D-value, explaining 2.7–6.5% of the phenotypic variances, in which 15 were likely to be novel. Three QTL, QGR.xjau-5AS, QCL.xjau-5AS and QD.xjau-5AS for GR, CL and D-value, respectively, at physical positions of 11.70–20.61 Mb between markers AX-111258240 and AX-94458300 on chromosome 5AS accounted for 3.4–4.8% of the phenotypic variances. Three QTL, QGP.xjau-5DL, QSH.xjau-5DL and QD.xjau-5DL for GP, SH and D-value, respectively, were flanked by markers AX-94524442 and AX-110998507 at 560.42–567.39 Mb on chromosome 5DL, accounting for 4.4–6.5% of the phenotypic variances. In addition, the candidate genes TraesCS5A02G022100, TraesCS5B02G014200 and TraesCS5D02G563900 were predicted. Based on transcriptional expression data, the results showed that the expression level of TaGATAs-5A, TaUbox-5B and TaGSTP-5D changed with the increase of treatment time under drought stress in tolerant and sensitive varieties. These are interesting targets in mining drought tolerance genes and the improvement of drought tolerance in wheat.

Beachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.

Wheat, a major food crop, faces significant yield constraints due to losses caused by various diseases, especially rusts and powdery mildew. Since the causal organisms are always evolving, there is a never-ending hunt for new genes/quantitative trait loci (QTLs) for resistance to control the damage. For this purpose, Triticum durum–Aegilops speltoides backcross introgression lines (DS-BILs) developed in our wide hybridization programme were screened against stripe rust and powdery mildew at both seedling and adult plant stages. DS-BILs showed complete to moderate resistance at the adult plant stage while varying resistance and susceptibility at the seedling stage. A total of 1095 single-nucleotide polymorphisms (SNPs) identified on 14 chromosomes of T. durum, using genotyping by sequencing, were used for QTL mapping. Eleven unique QTLs, across six chromosomes (chr1B, chr2A, chr2B, chr3B, chr6B and chr7B) were identified for resistance, four QTLs for field mixture of stripe rust pathotypes, two QTLs for stripe rust pathotype 78S84 and five QTLs for field mixture of powdery mildew pathotypes using stepwise regression-based likelihood ratio test for additive effect of markers and single-marker analysis. Eleven DS-BILs carrying multiple QTLs were identified which will serve as a useful resource to transfer the respective resistance to susceptible cultivars to develop all stage resistant elite cultivars where QTL for stripe rust resistance QYrAs.pau-2A.1 (LOD 3.8, PVE 24.51 linked to SNP S2A_16016633) and QTL for powdery mildew resistance QPmAs.pau-6B (logarithm of the odds (LOD) 3.2, phenotypic variation explained (PVE) 17.75 linked to SNP S6B_26793381) are major targets of the transfer.

The genetics of the root system is still not dissected for wheat and lack of knowledge prohibits the use of marker-assisted selection in breeding. To understand the genetic mechanism of root development, Synthetic W7984 × Opata M85 doubled-haploid (SynOpDH) mapping population was evaluated for root and shoot characteristics in PVC tubes until maturity. Two major quantitative trait loci (QTLs) for total root biomass were detected on homoeologous chromosomes 2A and 2D with logarithm of the odds scores between 6.25–10.9 and 11.8–20.86, and total phenotypic effects between 12.7–17.7 and 26.6–40.04% in 2013 and 2014, respectively. There was a strong correlation between days to anthesis and root and shoot biomass accumulation (0.50–0.81). The QTL for biomass traits on chromosome 2D co-locates with QTL for days to anthesis. The effect of extended vegetative growth, caused by photoperiod sensitivity (Ppd) genes, on biomass accumulation was always hypothesized, this is the first study to genetically support this theory.

This research communication describes a genome-wide association study for Italian buffalo mammary gland morphology. Three single nucleotide polymorphisms (AX-85117983, AX-8509475 and AX-85117518) were identified to be significantly associated with buffalo anterior teat length, posterior teat length and distance between anterior and posterior teat, respectively. Two significant signals for buffalo mammary gland morphology were observed in two genomic regions on the chromosome 10, and chromosome 20. One of the regions located on the chromosome 10 has the most likely candidate genes ACTC1 and GJD2, both of which have putative roles in the regulation of mammary gland development. This study provides new insights into the genetic variants of buffalo mammary gland morphology and may be beneficial for understanding of the genetic regulation of mammary growth.

Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations. Molecular information has resulted in gains in accuracy of between 0.05 and 0.27 and proved useful in parentage verification and the identification of QTLs for economically important traits. Except for a few established breeds with some degree of infrastructure, the basic building blocks to support conventional breeding programmes in small holder systems are lacking in most developing countries. In these systems, molecular data could offer quick wins in undertaking parentage verification and genetic evaluations using G matrix, and determination of breed composition. The development of next-generation molecular tools has prompted investigations on genome-wide signatures of selection for mainly adaptive and reproduction traits in SR in developing countries. Here, the relevance of the developments and application of GS and other molecular tools in developed countries to developing countries context is examined. Worth noting is that in the latter, the application of GS in SR will not be a ‘one-size fits all’ scenario. For breeds with some degree of conventional genetic improvement, classical GS may be feasible. In small holder systems, where production is key, community-based breeding programmes can provide the framework to implement GS. However, in fragile growth systems, for example those found in marginal environments, innovative GS to maximize adaptive diversity will be required. A cost-benefit analysis should accompany any strategy of implementing GS in these systems.

In this study, a near-isogenic line (BC4F10) CR572 developed by introgressing a chromosomal segment from Oryza rufipogon (accession no. 105491) into the Oryza sativa subsp. japonica cv. Hwaseong was found to exhibit a significant increase in the number of spikelets per panicle (SPP) and grain weight compared with the recurrent parent Hwaseong. Quantitative trait locus (QTL) analysis in F2 generation derived from the cross between CR572 and Hwaseong revealed that two QTLs, qSPP1 and qTGW1, were linked to a simple sequence repeat marker, RM283, on chromosome 1. The additive effect of the O. rufipogon allele at qSPP1 was 13 SPP, and 21.6% of the phenotypic variance was explained by the segregation of RM283. The qTGW1 QTL explained 19.1% of the phenotypic variance for grain weight. Substitution mapping was carried out with five F3 lines derived from F2 plants having informative recombination breakpoints within the target region. Substitution mapping indicated the linkage of qSPP1 and qTGW1. The grain yield of CR572 was 18.2 and 15.8% higher than that of Hwaseong at two locations, respectively, mainly due to the increase in 1000-grain weight and SPP. These results are very useful for QTL cluster transfer by molecular marker-assisted selection in rice breeding programmes and for QTL gene cloning by map-based cloning.

Recent progress has been achieved in the identification of quantitative trait loci (QTLs) and candidate genes, and they have been found to be very important for the production of chickens with more desirable meat characteristics. The major economic traits of chicken meat production were divided into two major categories, namely growth and carcass condition. In this paper, the QTL locations and candidate genes for the above mentioned traits are reviewed. The results presented here will provide guidelines for the selection of high quality and highly productive chickens through the marker assisted selection (MAS), which should be extensively used by poultry breeders and companies.

TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (P<0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/+ than +/+ lambs (−11.2%; P<0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).

Identification of the major loci responsible for insecticide resistance in malaria vectors would aid the development and implementation of effective resistance management strategies, which are urgently needed to tackle the growing threat posed by resistance to the limited insecticides available for malaria control. Genome-wide association studies in the major malaria vector, Anopheles gambiae, have been hindered by the high degree of within-population structuring and very low levels of linkage disequilibrium hence we revisited the use of quantitative trait loci (QTL) mapping to study resistance phenotypes in this vector species. Earlier work, identified two major QTL associated with pyrethroid resistance in A. gambiae s.s. from East Africa using genetic crossing of laboratory-colonized resistant and susceptible strains. In this study, we report the results from genetic mapping of pyrethroid resistance in three isofemale pedigrees established from wild-caught female A. gambiae s.s. mosquitoes from Benin. We identified two QTL on chromosomes 2L and 3R in these field populations, in similar genomic locations to the QTL identified in laboratory strains. The relative merits of two alternative study designs are discussed and suggestions made for future genetic mapping studies of insecticide resistance in mosquitoes.

Calreticulin (CRT) is a Ca2+-binding molecular chaperone in the endoplasmic reticulum. We cloned and characterized the CRT gene in an important marine food fish species Asian seabass (Lates calcarifer). The full-length DNA of the CRT gene was 2194 bp, including a complete open reading frame encoding 420 amino acid residues, a 113 bp 5′-untranslated region and an 818 bp 3′-untranslated region. The CRT gene contained nine exons and eight introns covering a total of 2772 bp genomic DNA from the start to stop codon. Ten single nucleotide polymorphisms (SNPs) were detected in introns and an exon in six individuals collected from five different locations. The CRT gene was assigned to linkage group 4 of the linkage map of Asian seabass. Quantitative real-time PCR revealed that the CRT gene was highly expressed in liver at the age of 1, 3 and 7 months under normal conditions, whereas its expression in liver reduced sharply after 0.5 to 2 h cold challenge at 16°C, and then increased slowly. A preliminary association analysis showed a significant (P < 0.001) association between the SNP6 in the CRT gene and the mortality after cold challenge at 16°C. Our results suggest that the CRT gene is associated with cold tolerance of Asian seabass and further investigation will be necessary to illustrate the underlying mechanisms.

The aim of this study was to test for the existence of causative genetic variation affecting body composition traits within or adjacent to the porcine insulin-like growth factor 2 (IGF2) gene beyond the known IGF2-intron3-G3072A mutation. A focussed quantitative trait loci analysis using four microsatellite markers within the telomeric region of porcine chromosome 2p was conducted in a large resource population comprising 2741 F2 offspring. The analysis of two subsets of animals that were alternatively homozygous for the in3G3072A mutation provides evidence for additional genetic variation significantly contributing to the overall quantitative trait nucleotide variance within our population.

An F2 cross between Duroc and Large White pigs was carried out in order to detect quantitative trait loci (QTL) for 11 meat quality traits (L*, a* and b* Minolta coordinates and water-holding capacity (WHC) of two ham muscles, ultimate pH of two ham and one loin muscles), 13 production traits (birth weight, average daily gain during post-weaning and fattening periods, carcass fat depths at three locations, estimated lean meat content, carcass length and weights of five carcass cuts) and three stress hormone-level traits (cortisol, adrenaline and noradrenaline). Animals from the three generations of the experimental design (including 456 F2 pigs) were genotyped for 91 microsatellite markers covering all the autosomes. A total of 56 QTL were detected: 49 reached the chromosome-wide level (suggestive QTL with a maximal probability of 0.05) and seven were significant at the genome-wide level (with a probability varying from 6 × 10−4 to 3 × 10−3). Twenty suggestive QTL were identified for ultimate pH, colour measurements and WHC on chromosome (SSC) 5, 6, 7, 8, 9, 11, 13, 14, 15 and 17. For production traits, 33 QTL were detected on all autosomes except SSC6, 8 and 9. Seven of these QTL, located on SSC2, 3, 10, 13, 16 and 17, exceeded the genome-wide significance threshold. Finally, three QTL were identified for levels of stress hormones: a QTL for cortisol level on SSC7 in the cortisol-binding globulin gene region, a QTL for adrenaline level on SSC10 and a QTL for noradrenaline level on SSC13. Among all the detected QTL, seven are described for the first time: a QTL for ultimate pH measurement on SSC5, two QTL affecting birth weight on SSC2 and 10, two QTL for growth rate on SSC15 (during fattening) and 17 (during post-weaning) and two QTL affecting the adrenaline and noradrenaline levels. For each QTL, only one to five of the six F1 sires were found to be heterozygous. It means that all QTL are segregating in at least one of the founder populations used in this study. These results suggest that both meat quality and production traits can be improved in purebred Duroc and Large White pigs through marker-assisted selection. It is of particular interest for meat quality traits, which are difficult to include in classical selection programmes.

Improving the fowl's natural ability to clear Salmonella from their body is important in reducing disease prevalence in poultry flocks, as recommended by a recent regulation of the European Commission. It may be efficient, as expected from estimation of heritability coefficients : 0.16 in chicks and 0.18 for global contamination of hens. The animal's age has to be considered since the genetic correlation between resistances at the two ages is negative. Selecting two series of divergent lines for increased or decreased resistance, after inoculation at one week of age (chick resistance) or at the peak of lay (adult resistance) confirmed the efficiency at least of selection for the adult resistance. In parallel, genes controlling variations to Salmonella resistance were researched and several QTLs identified in crosses between experimental lines and, for some of them, confirmed in commercial lines. Thanks to the derivation of a model of Salmonella propagation within a flock, it has been shown that a combination of vaccination and genetic selection can result in very low percentage of contamination.

Knowing the large difference in daily feed intake (DFI) between Large White (LW) and Piétrain (PI) growing pigs, a backcross (BC) population has been set up to map QTL that could be used in marker assisted selection strategies. LW × PI boars were mated with sows from two LW lines to produce 16 sire families. A total of 717 BC progeny were fed ad libitum from 30 to 108 kg BW using single-place electronic feeders. A genome scan was conducted using genotypes for the halothane gene and 118 microsatellite markers spread on the 18 porcine autosomes. Interval mapping analyses were carried out, assuming different QTL alleles between sire families to account for within breed variability using the QTLMap software. The effects of the halothane genotype and of the dam line on the QTL effect estimates were tested. One QTL for DFI (P < 0.05 at the chromosome-wide (CW) level) and one QTL for feed conversion ratio (P < 0.01 at the CW level) were mapped to chromosomes SSC6 – probably due to the halothane alleles – and SSC7, respectively. Three putative QTL for feed intake traits were detected (P < 0.06 at the CW level) on SSC2, SSC7 and SSC9. QTL on feeding traits had effects in the range of 0.20 phenotypic s.d. The relatively low number of QTL detected for these traits suggests a large QTL allele variability within breeds and/or low effects of individual loci. Significant QTL were detected for traits related to carcass composition on chromosomes SSC6, SSC15 and SSC17, and to meat quality on chromosome SSC6 (P < 0.01 at the genome-wide level). QTL effects for body composition on SSC13 and SSC17 differed according to the LW dam line, which confirmed that QTL alleles were segregating in the LW breed. An epistatic effect involving the halothane locus and a QTL for loin weight on SSC7 was identified, the estimated substitution effects for the QTL differing by 200 g between Nn and NN individuals. The interactions between QTL alleles and genetic background or particular genes suggest further work to validate QTL segregations in the populations where marker assisted selection for the QTL would be applied.