Half-sib Population Research Articles

Bright red passion fruit - evaluation of colorimetry and physicochemical quality for the fresh fruit market

The species Passiflora edulis Sims has varieties that produce fruits with colors that vary yellow to reddish purple and dark purple, all of which are well adapted to Brazil's varied climatic conditions. In the foreign market, demand is greatest for the variety Passiflora edulis f. edulis Sims, or pure purple passion fruit (gulupa), whose adaptation is more restricted to cool and upland regions. The Embrapa Cassava and Fruits research unit (Embrapa Mandioca e Fruticultura) generated a variety of passion fruit derived from P. edulis with reddish-purple fruits, aiming at the identification of genotypes with lower acidity and greater fruit sweetness to supply the fresh fruit market. A half-sib population of 83 P edulis genotypes, segregated for light red to purple and yellow color, was evaluated. For previous selection, the fruits were tested based on sweetness, and 67 genotypes were identified, while the other genotypes constituted the population of origin. Fruit weight, pulp and peel weight, juice yield, soluble solids content (SS), titratable acidity (TA) and SS/TA ratio were evaluated, in addition to colorimetric evaluation CIE-LAB (L*a*b*) . For physical traits, there was no significant difference between the pre-selected and original populations. For the chemical characteristics of the pulp, variation was observed only in titratable acidity (TA), which was 38% lower in the pre-selected population, resulting in a 43% increase in the SS/TA ratio. High correlations were not observed between the colorimetric parameters (L*, a* and b*) of the peel and pulp as well as TA and SS/TA. The heritability (h2) of the evaluated traits was high (66.40% to 86.25%), and 26 genotypes were chosen (ratio from 7.0 to 15.29) with 33.12% lower acidity and 39.84% higher ratio in the next selection cycle. These selected individuals are favorable to development of a passion fruit cultivar with sweeter flavor to supply the domestic and foreign fresh fruit markets.

Metabolomic Profiling in Combination with Data Association Analysis Provide Insights about Potential Metabolic Regulation Networks among Non-Volatile and Volatile Metabolites in Camellia sinensis cv Baijiguan.

The non-volatile and volatile metabolites in tea confer the taste and odor characteristics of tea fusion, as well as shape the chemical base for tea quality. To date, it remains largely elusive whether there are metabolic crosstalks among non-volatile metabolites and volatile metabolites in the tea tree. Here, we generated an F1 half-sib population by using an albino cultivar of Camellia sinensis cv Baijiguan as the maternal parent, and then we quantified the non-volatile metabolites and volatile metabolites from individual half-sibs. We found that the EGC and EGCG contents of the albino half-sibs were significantly lower than those of the green half-sibs, while no significant differences were observed in total amino acids, caffeine, and other catechin types between these two groups. The phenylpropanoid pathway and the MEP pathway are the dominant routes for volatile synthesis in fresh tea leaves, followed by the MVA pathway and the fatty acid-derivative pathway. The total volatile contents derived from individual pathways showed large variations among half-sibs, there were no significant differences between the albino half-sibs and the green half-sibs. We performed a comprehensive correlation analysis, including correlations among non-volatile metabolites, between volatile synthesis pathways and non-volatile metabolites, and among the volatiles derived from same synthesis pathway, and we identified several significant positive or negative correlations. Our data suggest that the synthesis of non-volatile and volatile metabolites is potentially connected through shared intermediates; feedback inhibition, activation, or competition for common intermediates among branched pathways may co-exist; and cross-pathway activation or inhibition, as well as metabolome channeling, were also implicated. These multiple metabolic regulation modes could provide metabolic plasticity to direct carbon flux and lead to diverse metabolome among Baijiguan half-sibs. This study provides an essential knowledge base for rational tea germplasm improvements.

Analysis of Transcriptome and Terpene Constituents of Scots Pine Genotypes Inherently Resistant or Susceptible to Heterobasidion annosum.

Root and stem rot caused by Heterobasidion annosum is a severe problem in boreal Scots pine. Dissecting the features of disease resistance is generally an essential step in resistance breeding in plants and forest trees. In this study, we explored inherent resistance factors of Scots pine against H. annosum. A total of 236 families consisting of 85 full-sib (FS), 35 half-sib population mix (HSpm), and 116 half-sib (HS) families of Scots pine seedlings were inoculated with a H. annosum isolate. We sampled needle tissues before inoculation for terpene measurements and RNA sequencing. Based on the lesion area, the extremes of 12 resistant and 12 susceptible families were selected for further analyses. Necrotic lesions resulting from fungal infection were in a weak to moderate relationship with the plant height. Monoterpenes were the principal terpene compounds observed in Scots pine seedlings. Concentrations of 3-carene were significantly higher in pine genotypes inherently resistant compared with susceptible seedlings. By contrast, susceptible genotypes had significantly higher proportions of α-pinene. Gene ontology analysis of differential expressed transcripts (DETs) revealed that response to biotic factors was enriched in resistant seedlings. Functional characterization of individual DETs revealed that higher expression of transcripts involved in response to abiotic stress was common in susceptible genotypes. This observation was supported by the annotation of hub genes in a key module that was significantly correlated with the lesion trait through weighted gene co-expression network analysis (WGCNA) of 16 HS and HSpm samples. These findings contribute to our understanding of constitutive resistance factors of Scots pine against Heterobasidion root and stem rot diseases.

Integer programming for selecting set of informative markers in paternity inference

BackgroundParentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms.ResultsHere, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy.ConclusionsWe present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT.

Genetic analysis of the early bud flush trait of tea plants (Camellia sinensis) in the cultivar 'Emei Wenchun' and its open-pollinated offspring.

The timing of bud flush (TBF) in the spring is one of the most important agronomic traits of tea plants (Camellia sinensis). In this study, we designed an open-pollination breeding program using ‘Emei Wenchun’ (EW, a clonal tea cultivar with extra-early TBF) as a female parent. A half-sib population (n = 388) was selected for genotyping using specific-locus amplified fragment sequencing. The results enabled the identification of paternity for 294 (75.8%) of the offspring, including 11 (2.8%) from EW selfing and 217 (55.9%) assigned to a common father, ‘Chuanmu 217’ (CM). The putative EW × CM full-sib population was used to construct a linkage map. The map has 4244 markers distributed in 15 linkage groups, with an average marker distance of 0.34 cM. A high degree of collinearity between the linkage map and physical map was observed. Sprouting index, a trait closely related to TBF, was recorded for the offspring population in 2020 and 2021. The trait had moderate variation, with coefficients of variation of 18.5 and 17.6% in 2020 and 2021, respectively. Quantitative trait locus (QTL) mapping that was performed using the linkage map identified two major QTLs and three minor QTLs related to the sprouting index. These QTLs are distributed on Chr3, Chr4, Chr5, Chr9, and Chr14 of the reference genome. A total of 1960 predicted genes were found within the confidence intervals of QTLs, and 22 key candidate genes that underlie these QTLs were preliminarily screened. These results are important for breeding and understanding the genetic base of the TBF trait of tea plants.

Breeding for Resilience to Water Deficit and Its Predicted Effect on Forage Mass in Tall Fescue

Resilience is increasingly part of the discussion on climate change, yet there is a lack of breeding for resilience per se. This experiment examined the genetic parameters of a novel, direct measure of resilience to water deficit in tall fescue (Lolium arundinaceum (Schreb.) Darbysh.). Heritability, genetic correlations, and predicted gain from selection were estimated for average productivity, resilience, and stability based on forage mass of a tall fescue half-sib population grown under a line-source irrigation system with five different water levels (WL). Resilience was both measurable and moderately heritable (h2 = 0.43), with gains of 2.7 to 3.1% per cycle of selection predicted. Furthermore, resilience was not correlated with average response over environments and negatively correlated with stability, indicating that it was not a measure of responsiveness to more favorable environments. Genetic correlations among WL ranged from 0.87 to 0.56, however in contrast, resilience was either not or slightly negatively genetically correlated with WL except for moderate correlations with the ‘crisis’ WL. Thus, breeding for improved resilience was predicted to have little effect on forage mass at any given individual water deficit environment. Overall, results indicated that this novel metric could facilitate breeding for improved resilience per se to water deficit environments.

The Genetic Basis for Salivary Gland Barriers to Arboviral Transmission.

Simple SummaryMosquito salivary glands are infected with an arbovirus prior to entering saliva. The virus in the mosquito’s saliva can then infect a vertebrate host when the vector acquires its next bloodmeal. Salivary gland infection and escape barriers (SGIB and SGEB, respectively) have been identified that modulate arbovirus transmission. SGIB are manifest as the absence of virus in the salivary glands of mosquitoes having a disseminated infection, while SGEB are evident as an absence of virus in the saliva of mosquitoes even though salivary glands are infected. The interaction between Aedes aegypti and viruses is dynamic and related to the genetic background of each vector population and virus variant. There is little understanding of the genetic basis for SGIB and SGEB. Here, nested, half-sib families of Aedes aegypti were used to estimate genetic and environmental variances, in which daughters from an individual dam differ in their phenotype due to the sire. We found that SGIB has a strong genetic basis with dengue virus infections but not with Zika or chikungunya virus infections, in which all salivary glands became infected. SGEB has a moderate genetic basis for Zika or chikungunya infections but not with dengue virus infections.Arthropod-borne viruses (arboviruses) infect mosquito salivary glands and then escape to saliva prior to virus transmission. Arbovirus transmission from mosquitoes can be modulated by salivary gland infection barriers (SGIBs) and salivary gland escape barriers (SGEBs). We determined the influence of SGIBs and SGEBs by estimating the quantitative genetic contributions of Aedes aegypti half-sib families (Mapastepec, Mexico) infected with three dengue 2 (DENV2), two chikungunya (CHIKV), and two Zika (ZIKV) genotypes. We determined virus titer per salivary gland and saliva at seven days post-infection and virus prevalence in the half-sib population. CHIKV or ZIKV genotypes did not present SGIB, whereas DENV2 genotypes showed low rates of SGIB. However, virus titer and prevalence due to additive genetic factors in the half-sib family displayed a significant narrow-sense heritability (h2) for SGIB in two of the three DENV2 genotypes and one CHIKV and one ZIKV genotype. SGEBs were detected in all seven virus strains: 60–88% of DENV2 and 48–62% of CHIKV or ZIKV genotype infections. SGEB h2 was significant for all CHIKV or ZIKV genotypes but not for any of the DENV2 genotypes. SGIBs and SGEBs exhibited classical gene-by-gene interaction dynamics and are influenced by genetic factors in the mosquito and the virus.

Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean (Glycine max (L.) Merr.)

AbstractCharacterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

Using the RTM-GWAS procedure to detect the drought tolerance QTL-allele system at the seedling stage under sand culture in a half-sib population of soybean [Glycine max(L.) Merr.

Soybean crops face drought as one of their major yield barriers. Dissecting the complete genetic architecture of drought tolerance (DT) is an ongoing challenge for soybean breeders. A half-sib population with 404 lines consisting of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) was established and tested for their DT under sand culture. The population was sequenced using RAD-seq (restriction-site-associated DNA sequencing) filtered with minor allele frequency (MAF) ≥ 0.01, and 55 936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The innovative RTM-GWAS (restricted two stage multi-locus genome-wide association study) identified 46 novel QTLs with 107 alleles on an average of 38.67% of the phenotypic variance (PV) collectively for relative plant length (RPL) and relative plant dry weight (RPDW). The identified quantitative trait loci (QTLs) with their corresponding alleles for RPL and RPDW were structured into QTL-allele matrices, showing the DT genetic architecture of the three parents and half-sib population. From the matrices, the possible best genotype was predicted to have their weighted average value (WAV) over two indicators 1.663, while the top 10 optimal crosses among RILs with 95thpercentile WAV was 0.872–0.960, transgressive over the parents (0.469–0.675) but much less than 1.663, depicting further pyramiding potential. From the detected QTL-allele system, 63 potential candidate genes collectively for both RPL and RPDW indicators explaining on average of 26.94% PV were annotated and χ2-tested as a DT potential candidate gene system involving nine biological processes, endorsing the genetic complexity of DT.

The degree of phenotypic variation of morphological and agronomic characters of eight F1 populations of cassava (Manihot esculenta) at Bandar Lampung

Utomo SD, Yusartika P, Popy L, Edy A, Sunyoto, Ardian. 2018. The degree of phenotypic variation of morphological and agronomic characters of eight F1 populations of cassava (Manihot esculenta) at Bandar Lampung. Pros Sem Nas Masy Biodiv Indon 4: 39-46. The objective of this study was to estimate the degree of phenotypic variation (DPV) of morphological and agronomic characters of eight F1 populations of cassava the results of natural sexual hybridization and/or self of 80 parental clones; the eight populations was derived from female parents UJ 5, Cimanggu, UJ 3, Klenteng 37, Mulyo 3, BL1, BL 4 and Darul Hidayah. The pollination was conducted in 2015 at highland Sekincau, West Lampung (1100 m asl.). The morphological and agronomic characters included qualitative and quantitative characters. Study to estimate the was conducted at Bandar Lampung, from May 2016-March 2017. The DPV of quantitative characters were high if the percentage of recombinant phenotypes > 67%, moderate if 33%≤DPV≤67, and low if DPV 2 x Interquartile Range (IQR) dan low if the total Range ≤ 2 x IQR. Quantitative characters color of apical leaves, color of adaxial petiole, and color of abaxial petiole of all populations showed DPV high or moderate. All quantitative characters observed (number of leaf lobus, length of leaf lobus, width of leaf lobus, length/width ratio of leaf lobus, length of petiole, and starch rendement) indicated DPV high on F1 half-sib population of UJ5, UJ3, BL1, dan BL4. Except for the length of leaf lobus and starch rendement, all quantitative characters showed high DPV on population of Cimanggu and Darul Hidayah; DPV of length of leaf lobus and starch rendement was low. The high variation of most qualitative and quantitative characters indicated that the open/natural hybridization among parental clones occurred and was effective to produce recombinant phenotypes.

Terpenes associated with resistance against the gall wasp, Leptocybe invasa, in Eucalyptus grandis.

Leptocybe invasa is an insect pest causing gall formation on oviposited shoot tips and leaves of Eucalyptus trees leading to leaf deformation, stunting, and death in severe cases. We previously observed different constitutive and induced terpenes, plant specialized metabolites that may act as attractants or repellents to insects, in a resistant and susceptible clone of Eucalyptus challenged with L.invasa. We tested the hypothesis that specific terpenes are associated with pest resistance in a Eucalyptus grandis half-sib population. Insect damage was scored over 2 infestation cycles, and leaves were harvested for near-infrared reflectance (NIR) and terpene measurements. We used Bayesian model averaging for terpene selection and obtained partial least squares NIR models to predict terpene content and L.invasa infestation damage. In our optimal model, 29% of the phenotypic variation could be explained by 7 terpenes, and the monoterpene combination, limonene, α-terpineol, and 1,8-cineole, could be predicted with an NIR prediction ability of .67. Bayesian model averaging supported α-pinene, γ-terpinene, and iso-pinocarveol as important for predicting L.invasa infestation. Susceptibility was associated with increased γ-terpinene and α-pinene, which may act as a pest attractant, whereas reduced susceptibility was associated with iso-pinocarveol, which may act to recruit parasitoids or have direct toxic effects.

Estimates of genetic parameters for fatty acid compositions in the longissimus dorsi muscle of Hanwoo cattle

We estimated the heritabilities (h2) and genetic and phenotypic correlations among individual and groups of fatty acids, as well as their correlations with six important carcass and meat-quality traits in Korean Hanwoo cattle. Meat samples were collected from the longissimus dorsi muscles of 1000 Hanwoo steers that were 30-month-old (progeny of 85 proven Hanwoo bulls) to determine intramuscular fatty acid profiles. Phenotypic data on carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), marbling score (MS), Warner–Bratzler shear force (WBSF) and intramuscular fat content (IMF) were also investigated using this half-sib population. Variance and covari.ance components were estimated using restricted maximum likelihood procedures under univariate and pairwise bivariate animal models. Oleic acid (C18:1n-9) was the most abundant fatty acid, accounting for 50.69% of all investigated fatty acids, followed by palmitic (C16:0; 27.33%) and stearic acid (C18:0; 10.96%). The contents of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs) were 41.64%, 56.24% and 2.10%, respectively, and the MUFA/SFA ratio, PUFA/SFA ratio, desaturation index (DI) and elongation index (EI) were 1.36, 0.05, 0.59 and 0.66, respectively. The h2 estimates for individual fatty acids ranged from very low to high (0.03±0.14 to 0.63±0.14). The h2 estimates for SFAs, MUFAs, PUFAs, DI and EI were 0.53±0.14, 0.49±0.14, 0.23±0.10, 0.51±0.13 and 0.53±0.13, respectively. The genetic and phenotypic correlations among individual fatty acids and fatty acid classes varied widely (−0.99 to 0.99). Notably, C18:1n-9 had favourable (negative) genetic correlations with two detrimental fatty acids, C14:0 (−0.76) and C16:0 (−0.92). Genetic correlations of individual and group fatty acids with CWT, EMA, BFT, MS, WBSF and IMF ranged from low to moderate (both positive and negative) with the exception of low-concentration PUFAs. Low or near-zero phenotypic correlations reflected potential non-genetic contributions. This study provides insights on genetic variability and correlations among intramuscular fatty acids as well as correlations between fatty acids and carcass and meat-quality traits, which could be used in Hanwoo breeding programmes to improve fatty acid compositions in meat.

Tall fescue forage mass in a grass-legume mixture: predicted efficiency of indirect selection

High fertilizer prices and improved environmental stewardship have increased interest in grass-legume mixed pastures. It has been hypothesized, but not validated, that the ecological combining ability between grasses and legumes can be improved by breeding specifically for mixture performance. This experiment examined the predicted efficiency of selection in a grass monoculture environment to indirectly improve tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) forage mass in a grass-legume mixture. Heritability, genetic and rank correlations, and selection efficiencies were estimated for forage mass in a tall fescue half-sib population grown as spaced-plants overseeded with either turf-type tall fescue (monoculture) or alfalfa (mixture). Heritability for tall fescue forage mass in monoculture ranged from 0.32 to 0.70 and were always similar or greater than those in mixture (range 0.27–0.55) for four successive harvests and annual total. Genetic correlations between monoculture and mixture tall fescue forage mass varied with values of 0.48, 0.92, −0.31, 0.70, and 0.25 in June, July, August, October, and annual total, respectively. Indirect selection efficiencies exceeded or approached direct selection for mixtures only in July and October (1.29, and 0.73, respectively). Whereas, indirect selection efficiencies were low in June, August, and annual forage mass (0.58, −0.31, and 0.28, respectively). Moreover, low Spearman’s rank correlations (−0.03 to 0.35) indicated differing half-sib family performance between the monoculture and mixture environments. Results indicate that direct selection should be used to improve tall fescue forage mass in a grass-legume mixture, and support the hypothesis of increasing ecological combining ability by breeding for mixtures per se.

Effect of Recurrent Selection on Drought Tolerance and Related Morpho-Physiological Traits in Bread Wheat.

Drought is one of the major abiotic stresses affecting wheat yield. A recurrent selection program was conducted to improve the drought tolerance and yield of bread wheat using drought tolerant advanced breeding lines from a drought tolerant x susceptible cross (HI 1500 x HUW 510). The parental lines were evaluated for yield, biomass and harvest index (HI) in addition to the drought adaptive traits like Canopy Temperature (CT), chlorophyll content and Normalized Difference Vegetative Index (NDVI). After three rounds of recurrent selection, the half sib progenies exhibited a marked reduction in CT, chlorophyll content and biomass; whereas improvement was noted for yield, HI and NDVI. Drought tolerance of the half-sib population appeared enhanced as indicated by drought indices and grain yield. Compared to base population, half-sibs showed better HI, grain filling and a significant (17.1%) increase in grain yield under water stress conditions. Cooler canopies and increased early vigour might have contributed to drought tolerance. A favourable combination of gibberellin sensitive and insensitive Rhtalleles was observed in the recombinant progenies. However, increased yield under water stress had a negative trade off in reduction of biomass. The study also identified potential lines with high yield and drought tolerance for subsequent varietal development for water limited areas.

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array.

BackgroundPersistence of gastrointestinal nematode (GIN) infection and the related control methods have major impacts on the sheep industry worldwide. Based on the information generated with the Illumina OvineSNP50 BeadChip (50 K chip), this study aims at confirming quantitative trait loci (QTL) that were previously identified by microsatellite-based genome scans and identifying new QTL and allelic variants that are associated with indicator traits of parasite resistance in adult sheep. We used a commercial half-sib population of 518 Spanish Churra ewes with available data for fecal egg counts (FEC) and serum levels of immunoglobulin A (IgA) to perform different genome scan QTL mapping analyses based on classical linkage analysis (LA), a combined linkage disequilibrium and linkage analysis (LDLA) and a genome-wide association study (GWAS).ResultsFor the FEC and IgA traits, we detected a total of three 5 % chromosome-wise significant QTL by LA and 63 significant regions by LDLA, of which 13 reached the 5 % genome-wise significance level. The GWAS also revealed 10 significant SNPs associated with IgAt, although no significant associations were found for LFEC. Some of the significant QTL for LFEC that were detected by LA and LDLA on OAR6 overlapped with a highly significant QTL that was previously detected in a different half-sib population of Churra sheep. In addition, several new QTL and SNP associations were identified, some of which show correspondence with effects that were reported for different populations of young sheep. Other significant associations that did not coincide with previously reported associations could be related to the specific immune response of adult animals.DiscussionOur results replicate a FEC-related QTL located on OAR6 that was previously reported in Churra sheep and provide support for future research on the identification of the allelic variant that underlies this QTL. The small proportion of genetic variance explained by the detected QTL and the large number of functional candidate genes identified here are consistent with the hypothesis that GIN resistance/susceptibility is a complex trait that is not determined by individual genes acting alone but rather by complex multi-gene interactions. Future studies that combine genomic variation analysis and functional genomic information may help elucidate the biology of GIN disease resistance in sheep.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0182-4) contains supplementary material, which is available to authorized users.

A combined coalescence gene-dropping tool for evaluating genomic selection in complex scenarios (ms2gs).

We present ms2gs, a combined coalescence - gene dropping (i.e. backward-forward) simulator for complex traits. It therefore aims at combining the advantages of both approaches. It is primarily conceived for very short term, recent scenarios such as those that are of interest in animal and plant breeding. It is very flexible in terms of defining QTL architecture and SNP ascertainment bias, and it allows for easy modelling of alternative markers such as RADs. It can use real sequence or chip data or generate molecular polymorphisms via the coalescence. It can generate QTL conditional on extant molecular information, such as low-density genotyping. It models (simplistically) sequence, imputation or genotyping errors. It requires as input both genotypic data in plink or ms formats, and a pedigree that is used to perform the gene dropping. By default, it compares accuracy for BLUP, SNP ascertained data, sequence, and causal SNPs. It employs VanRaden's linear (GBLUP) and nonlinear method for incorporating molecular information. To illustrate the program, we present a small application in a half-sib population and a multiparental (MAGIC) cross. The program, manual and examples are available at https://github.com/mperezenciso/ms2gs.

Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.)

Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.

QTL mapping in outbred half-sib families using Bayesian model selection

In this article, we propose a model selection method, the Bayesian composite model space approach, to map quantitative trait loci (QTL) in a half-sib population for continuous and binary traits. In our method, the identity-by-descent-based variance component model is used. To demonstrate the performance of this model, the method was applied to map QTL underlying production traits on BTA6 in a Chinese half-sib dairy cattle population. A total of four QTLs were detected, whereas only one QTL was identified using the traditional least square (LS) method. We also conducted two simulation experiments to validate the efficiency of our method. The results suggest that the proposed method based on a multiple-QTL model is efficient in mapping multiple QTL for an outbred half-sib population and is more powerful than the LS method based on a single-QTL model.

Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme

The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-limiting enzyme in the biosynthesis of cholesterol. We have studied the role of the HMGCR gene in pig lipid metabolism by means of expression and structural analysis. We describe here the complete coding region of this gene in pigs and report two synonymous single nucleotide polymorphisms in the coding region. We have, additionally, studied the association of one of these polymorphisms (HMGCR:c.807A>C) with several lipid deposition- and cholesterol-related traits in a half-sib population generated from a commercial Duroc line, showing in some families a positive relationship of HMGCR:c.807A allele with serum low-density lipoprotein (LDL)-bound cholesterol and triglyceride levels, and also with intramuscular fat (IMF) content of gluteus medius muscle. We have also assessed the expression levels in muscle and in liver from 68 Duroc individuals corresponding to the most extreme animals for the analysed traits. Liver HMGCR expression correlated negatively with the serum high-density lipoprotein (HDL) levels, carcass lean percentage and stearic acid content, while muscle expression correlated also negatively with the carcass lean percentage, stearic and linoleic acids content, but showed a positive correlation with the serum lipid cholesterol (HDL, LDL and total cholesterol), IMF and muscle oleic and palmitic fatty acid content. With this information, we have performed an association analysis of expression data with lipid metabolism phenotypic levels and the HMGCR genotype. The results indicate that HMGCR expression levels in muscle are different in the two groups of pigs with extreme values for fat deposition and total cholesterol levels, and also between animals with the different HMGCR genotypes.

A QTL that confers resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]) in tetraploid potato populations segregating for leptine

Genetic resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]) from Solanum chacoense has been incorporated in the tetraploid potato selection, ND4382-19, which is highly resistant and contains moderate level of foliar leptines. We recently reported using ND4382-19 progeny, population ND5873 (ND4382-19 x Chipeta), to map two genes that segregated as complementary epistatic genes that allow accumulation of leptinidine (Lep) and acetyl-leptinidine (AL) on chromosomes 2 and 8, respectively. We describe here the characterization of a second half-sib population NDG116 (ND4382-19 x N142-72). In this population, solasodine from parent N142-72, which has Solanum berthaultii in its background, was predominant over solanidine-based alkaloids. Concentrations of solanidine, leptinidine, and acetyl-leptinidine were 15-, 5-, and 14-fold lower than in the ND5873 population. Nevertheless, Lep and AL mapped to the same locations on chromosomes 2 and 8 of parent ND4382-19, respectively. The two populations were evaluated for resistance to Leptinotarsa in field assays, and by detached leaf assay for population NDG116. In both families, QTL analysis identified a major QTL from ND4382-19 on the distal end of chromosome 2, close to the Lep locus. The contribution of this QTL to resistance ranged from 11 to 34% for ND5873 at four field sites. Contribution to resistance from the linkage group that contains the gene AL for the accumulation of leptine was not detected. In family NDG116, the same chromosome 2 QTL was detected for field and detached leaf assays, explaining 26 and 12% of the variance for defoliation and larval development, respectively. These data may indicate another resistance mechanism besides leptine in the Leptinotarsa resistance observed in these populations.