Full-sib Families Research Articles

Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits.

With climate change, the pressure on tree breeding to provide varieties with improved resilience to biotic and abiotic stress is increasing. As such, pest resistance is of high priority but has been neglected in most tree breeding programs, given the complexity of phenotyping for these traits and delays to assess mature trees. In addition, the existing genetic variation of resistance and its relationship with productivity should be better understood for their consideration in multitrait breeding. In this study, we evaluated the prospects for genetic improvement of the levels of acetophenone aglycones (AAs) in white spruce needles, which have been shown to be tightly linked to resistance to spruce budworm. Furthermore, we estimated the accuracy of genomic selection (GS) for these traits, allowing selection at a very early stage to accelerate breeding. A total of 1,516 progeny trees established on five sites and belonging to 136 full‐sib families from a mature breeding population in New Brunswick were measured for height growth and genotyped for 4,148 high‐quality SNPs belonging to as many genes along the white spruce genome. In addition, 598 trees were assessed for levels of AAs piceol and pungenol in needles, and 578 for wood stiffness. GS models were developed with the phenotyped trees and then applied to predict the trait values of unphenotyped trees. AAs were under moderate‐to‐high genetic control (h 2: 0.43–0.57) with null or marginally negative genetic correlations with other traits. The prediction accuracy of GS models (GBLUP) for AAs was high (PAAC: 0.63–0.67) and comparable or slightly higher than pedigree‐based (ABLUP) or BayesCπ models. We show that AA traits can be improved and that GS speeds up the selection of improved trees for insect resistance and for growth and wood quality traits. Various selection strategies were tested to optimize multitrait gains.

Effect of high temperature during larval and juvenile stages on masculinization of common carp (Cyprinus carpio, L)

Temperature can influence sex differentiation in gonochoristic fish with a genetic sex-determination system (GSD). The precise effect of high temperature on sex remains unknown in a eurythermal carp (Cyprinus carpio). The present study aimed to identify the critical thermosensitive period and the effect of temperature on sex differentiation in common carp, C. carpio. Our results demonstrated the lower and upper limits of the lethal maximum temperature (LTmax) of C. carpio juveniles (42 dph) were 37.2 and 39.7 °C, respectively in the present study condition. The confidence limit of the median lethal time (LT50) of the juveniles was 38.87 °C. To determine the thermosensitivity of sex differentiation, the larvae were exposed to a high temperature (36 °C) for 7-day durations, starting from hatching until 69 dph. The period of critical thermosensitivity for sex differentiation towards the male phenotype was 7 to 13 dph. The sex proportions and thermosensitivity of sex differentiation illustrated high inter-familial variability of sex ratio skewed towards male phenotype ranged from 69 to 100% in the 10 full-sib families exposed to 36 °C. Exposure of juveniles to the high temperatures (34 °C and 36 °C) significantly altered the sex ratios and produced 63 to 82 % male phenotype even during the transition of sex differentiation. This study demonstrates that sex differentiation in common carp is seriously influenced by the environmental process. Also, it explores a temperature-induced method of skewing sex ratio towards the male phenotype irrespective of morphological gonad differentiation in common carp.

Inheritance of static bending properties and classification of load-deflection curves in Cryptomeria japonica

Abstract To clarify inheritance of static bending properties in relation to elastic and plastic regions, air-dry density, microfibril angle of the S2 layer in latewood tracheid (MFA), and static bending properties (modulus of elasticity [MOE], modulus of rupture [MOR] and bending work) were examined for juvenile wood of 18 full-sib families in 20-year-old Cryptomeria japonica. Heritability of all traits ranged from 0.12 (bending work) to 0.51 (air-dry density). Based on the results from principal component analysis (PCA) and cluster analysis, the families were classified into four groups with different types of load-deflection curves, suggesting that both elastic properties and deflection in plastic region differed among families. Furthermore, families included in a group were produced from specific parents, suggesting that deflection in plastic region as well as elastic property is inheritable. It can be concluded that mating parents may affect elasticity and plasticity of offspring.

Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

BackgroundFruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40–46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles.ConclusionsA multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.

Genetic variation among full-sib families and the effect of non-genetic factors on growth traits at harvest in Clarias magur (Hamilton, 1822)

Magur (Clarias magur) is an Indian catfish species with a good potential for aquaculture. The expansion of magur aquaculture is hindered because of low reproductive and survival rates. Furthermore, males need to be sacrificed to collect milt for artificial fertilization. At present, magur seed production mainly depends on the wild-caught juveniles and to a smaller extent, from broodfish whose genetic potential is unknown. The availability of high-quality seeds in a sustainable way can be ensured through the selective breeding program for magur. The knowledge of factors influencing growth traits and their genetic parameters is a pre-requisite for implementing a genetic selection program. The present study aimed to quantify the performance of C.magur reared in a two-year class and estimate their heritabilities at stocking and harvest and also to estimate the genetic and phenotypic correlations among them. The growth traits such as Body Weight (BW), Total Length (TL), Body Depth (BD), Head Width (HW), and Average Daily Gain (ADG) were recorded from 1413 animals belonging to 78 fullsib families produced by adopting single pair mating design, after one year of pond culture (traits at harvest). Genetic parameters were also estimated for body weight (BW0) and total length (TL0) measured from 2328 fish from 78 fullsib families at the time of stocking. Magur attained an average BW of 135 g and 24.5 cm TL after one year culture period. The heritabilities of BW, TL, and ADG were 0.44 ± 0.07, 0.32 ± 0.06, and 0.42 ± 0.07, respectively and may be biased upwardly due to the single pair mating design. Genetic correlations between harvest traits were all positive and varied in magnitude between traits (0.74 to 0.99). The results obtained from the current study indicate the presence of genetic variation in magur population for growth traits and selection based on genetic merit can produce improvement in these traits.

The identification of a major sex QTL in the white-leg shrimp, Litopenaeus vannamei

The white-leg shrimp, Litopenaeus vannamei, is the most widely farmed shrimp species globally. In recent years, interest in developing selective breeding programs and identifying the mechanisms controlling sex determination in L. vannamei has increased in the hope that improvements can be made on productivity efficiency. L. vannamei exhibits sexual dimorphism whereby females grow faster and larger than males. The discovery of novel genes or regions involved in sex-determination within L. vannamei would allow farmers to exploit this natural sexual dimorphism to enhance productivity. This study utilised a revised genetic linkage map for L. vannamei (whereby linkage groups 42 and 44 were merged as LG42.44) to conduct QTL and GWAS analyses from 20 full-sib families to identify one major QTL across 20 mapping families. The QTL was identified on LG42.44 and had a 95% confidence interval of 0–12.7 cM across all families (428 progeny). This region explained from 79.4–100% of the phenotypic variation. Independent genome wide association studies (GWAS) across 1952 individuals identified 11 significant SNPs (in high linkage disequilibrium) located on LG42.44 (0–12.7 cM) with one SNP 5790_511 with an extreme -log10 (P-value) of 294. For SNP 5790_511, 93% of homozygous genotypes were males and 97.6% of heterozygous were females indicating relatively close proximity of this SNP to the sex-determination locus. The SNP heritability for the sex phenotype was 0.84 +-0.007 suggesting a strong genetic basis of sex determination. A previously described feminisation gene, Pvfem-1, characterised as being involved in male and female gonad differentiation, was annotated to LG16; however no significant associations or QTL for sex were identified at this region in this study. Even though no known sex-determination genes could be identified under the QTL region of LG42.44, the large proportion of phenotypic variance explained by the significantly associated markers underlying the QTL region is promising and highlights this region for further fine mapping and sex-determination gene discovery efforts.

Indication of Quantitative Multiple Disease Resistance to Foliar Pathogens in Pinus radiata D.Don in New Zealand.

Increasing resistance against foliar diseases is an important goal in the Pinus radiata D.Don breeding program in New Zealand, and screening for resistance has been in place for some time, since the late 1960s. The current study presents results of four progeny trials within the breeding program to investigate whether multiple disease resistance could be detected against three different needle diseases in P. radiata: Dothistroma needle blight (DNB) caused by Dothistroma septosporum, Cyclaneusma needle cast (CNC) caused by Cyclaneusma minus, and red needle cast (RNC) caused by Phytophthora pluvialis. Four progeny trials in the North Island of New Zealand were available to estimate heritabilities and between-trait genetic correlations. Two of the trials were assessed for DNB, involving 63 full-sib families. A third trial was assessed for CNC, involving 172 half-sib families, and a fourth trial was assessed for RNC, involving 170 half-sib families. Disease resistances had moderate estimates of heritability (0.28–0.48) in all trials. We investigated the potential for multiple disease resistance to the three foliar diseases by estimating genetic correlations between disease resistances using a spatial linear mixed model. The correlation between DNB and CNC resistance was favorable and strong (0.81), indicating that genotypes that are highly resistant to DNB also have a high resistance to CNC. These results suggest that selection based on resistance to DNB could allow for simultaneous indirect selection for resistance to CNC, usually only expressed at a later age. This would allow selections to be made earlier due to the earlier expression of DNB than CNC and reduce the number of expensive disease assessments being undertaken. Conversely, genetic correlation estimates for RNC with DNB and CNC were close to zero, and very imprecise. As such, later-age assessments for this disease would still be required.

Novel insights into the selective breeding for disease resistance to vibriosis by using natural outbreak survival data in Chinese tongue sole (Cynoglossus semilaevis)

As an important farmed flatfish species, Chinese tongue sole (Cynoglossus semilaevis) is heavily threatened by vibriosis in recent years. Genetic selection for disease resistance is a sustainable and effective approach to reduce frequent outbreaks. To verify whether the resistance of vibriosis (caused by co-infections of different Vibrio spp. in natural outbreak) can be included in breeding programs, in this study, genetic analysis of resistance to vibriosis based on natural outbreak survival data was carried out by using four statistical models (three cross-sectional models and one longitudinal model). The magnitude of the genetic variation in the resistance of vibriosis was estimated through a 56-day natural outbreak test of 15,912 individuals from 78 full-sib families (the offspring of 77 sires and 78 dams). Variance components and heritabilities were estimated at two cut-off points respectively, i.e. day 35 with 49.2% cumulative mortality and day 56 with 71.6% finial cumulative mortality. Heritabilities of resistance to vibriosis were low to moderate, where values at day 56 (0.04–0.21) were significantly different from zero, while values at day 35 (0.03–0.10) were not significantly different from zero in each corresponding model. The Spearman rank correlations between family EBVs for different models were high (> 0.98), indicating a nearly identical ranking of families. Compare to three simpler cross-section models, the longitudinal model taken the time until death into account demonstrated the highest accuracy of family selection. These results confirmed the existence of genetic variation for resistance to vibriosis and provided novel insights into the selective breeding for disease resistance to vibriosis by using natural outbreak survival data in tongue sole.

First high-resolution genetic linkage map of taimen (Hucho taimen) and its application in QTL analysis of growth-related traits

Taimen (Hucho taimen) is an excellent aquaculture species. Currently, no selective breeding program has been conducted. To promote molecular breeding for taimen, we used genotype-by-sequencing technology to construct a high-resolution linkage map and performed QTL studies of growth-related traits. We sequenced 177 individuals of two full-sib families and obtained 58,016 SNPs. Among them, 30,535 SNPs were assigned to 42 linkage groups. The linkage map contained 6734 unique loci and spanned 4253.484 cM in total, with an average interval distance of 0.657 cM. The length for each linkage group ranged from 66.257 cM to 135.533 cM, with an average interval distance of 0.468 cM to 1.110 cM. This SNP linkage map integrated 65.1% scaffolds of the Hucho hucho genome to form 42 pseudo-chromosomes, with a mean correlation coefficiency of 0.893 between the linkage map and the genome. Based on this high-resolution linkage map, we performed QTL analyses of four growth-related traits of taimen aged 6–7 months. The analyses discovered 27 QTLs, including 18 QTLs for body weight, 5 QTLs for standard length, 3 QTLs for body thickness, and 1 QTL for body height. Based on Hucho hucho genome annotation, 487 genes within QTL regions were enriched in metabolism-related pathways; these genes could serve as candidate genes associated with the growth of taimen. The linkage map and QTLs obtained in this study provide useful tools for genetic studies and molecular breeding of taimen.

Variation analyses of controlled pollinated families and parental combining ability of Pinus koraiensis

To evaluate and select elite Pinus koraiensis parent combinations and offspring families, 34 full-sib families were evaluated. Variance analysis of tree height, diameter at breast height and volume showed no significant differences among each block, the interaction of block, male and female. The family heritability of all traits were high (> 0.9). Phenotypic and genotypic coefficients of variance of height, diameter at breast height, and volume showed that the phenotypic coefficient of variation of volume in the same combination was higher than height and diameter at breast height, indicating that volume was the main factor determining excellent single plant selection. The female and male trees with the best general combining ability indicated that the optimal parental hybridization was not necessarily the optimal combination. In addition, the least parents of hybrid offspring performance were always relatively poor and should not be selected as hybrid parents. Additionally, we found there was no significant difference among the effects of female and male parents by random modelling, but there were significant differences by fixed modelling. The most significant effect of female- and male interaction, and the selection of better female or male parents in the test parent group should be efficient as well as the results of significant variation among them by fixed modelling. For the evaluated breeding population of P. koraiensis, the backward selection of excellent parent combinations or forward selection of excellent individuals as progeny should be the major breeding strategies.

Quantitative trait loci and genes associated with salmonid alphavirus load in Atlantic salmon: implications for pancreas disease resistance and tolerance

Salmonid alphavirus infection results in pancreas disease causing severe economic losses for Atlantic salmon aquaculture. Knowledge about genes and pathways contributing to resistance is limited. A 54 K SNP panel was used to genotype 10 full-sibling families each consisting of ~ 110 offspring challenged with salmonid alphavirus subtype 3. Relative heart viral load was assessed at 4- and 10-weeks post-infection using quantitative PCR. A moderate genomic heritability of viral load at 4 weeks (0.15–0.21) and a high positive correlation with survival (0.91–0.98) were detected. Positions of QTL detected on chromosome 3 matched those for survival detected by other studies. The SNP of highest significance occurred in the 3′ untranslated region of gig1, a fish-specific antiviral effector. Locus B of immunoglobulin heavy chain mapped to an area containing multiple SNPs with genome-wide association. Heart mRNA-seq comparing parr from families with high- versus low-genomic breeding value, and matching sample genotypes for SNPs, identified two eQTL for salmonid alphavirus load. Immune genes associated with trans-eQTL were numerous and spread throughout the genome. QTL regions contained several genes with known or predicted immune functions, some differentially expressed. The putative functional genes and variants identified could help improve marker-based selection for pancreas disease resistance.

Crossbreeding of three different shell color lines in the Pacific oyster reveals high heterosis for survival but low heterosis for growth

Heterosis is important for improving productive traits in aquaculture, but the heterosis between selected lines remains unclear in bivalve molluscs. Here, a diallel crosses among black shell (B, 7th generation), white shell (W, 7th generation) and orange shell (O, 6th generation) lines of the Pacific oyster were performed to examine the potential for exploiting heterosis of productive traits by crossbreeding of selected lines. Heterosis and combining abilities for growth and survival of 27 full-sib families were analyzed at both larval and juvenile stages, of which the juvenile stage was examined at two environments (Rongcheng and Rushan) for 10 months. The variance of specific combining ability accounts for the majority of the total variance for larval and juvenile survival and juvenile growth, which revealed the importance of non-additive genetic effects (heterosis) among these lines. Moreover, all reciprocal hybrids showed low or no heterosis for growth at both larval and juvenile stages, but a high heterosis for larval survival. This finding suggested that inter-line crossbreeding can be applied to improve the larval survival in hatcheries. Furthermore, four of six hybrid crosses showed positive HPH in Rushan but negative HPH in Rongcheng. The higher HPH at Rushan suggested that inter-line crossbreeding in C. gigas has more application value in Rushan. In addition, the survival of both black shell and white shell lines have been improved by crossing with the orange shell line. Especially, the hybrid cross WO (W♀ × O♂) can improve the survival rate of purebred WW by nearly 130% at larval stage and nearly 40% at juvenile stage. Overall, this study reveals the high heterosis for survival among selected lines in the Pacific oyster, and will be helpful for the utilization of non-additive genetic effects among existing selected lines in bivalves.

Novel Benedenia disease resistance QTLs in five F1 families of yellowtail (Seriola quinqueradiata)

Benedenia disease is a parasitic disease occurring in cultured marine fish which is caused by the ectoparasite, Benedenia seriolae. This parasitic disease causes serious damage to yellowtail culture due to secondary infections, however prevention methods for the ectoparasite have limited efficacy. Thus, we attempted to initiate a marker-assisted selection (MAS) program to produce a yellowtail strain that has resistance to Benedenia disease. In this study, we conducted a genome scan for quantitative trait loci (QTL) that affect Benedenia disease resistance in five full-sib families using 7910 SNP markers. Sex-specific linkage maps was constructed for the five families and the total number of markers on each map was ranged from 1115 to 1427. We found four significant and five suggestive QTLs affecting Benedenia disease resistance. The phenotypic variation explained (PVE) by each QTL ranged from 8.2% to 29.6%. The QTL with a PVE of 29.6% on LG Squ6 in the family Rr1 was considered to be the major QTL. Novel Benedenia disease resistance QTLs detected in this study enhance our understanding of the genes and genomic regions related to Benedenia disease resistance in yellowtail and can serve as a basis for MAS breeding.

Pollination Bag Type Has a Significant Impact on Cone Survival in Mass Production of Controlled Pollinated Seeds in Loblolly Pine

Abstract Since 2009, deployment of full-sib families of loblolly pine (Pinus taeda L.) has gained prominence in the southeastern United States. To produce full-sib seed, a pollination bag is used to isolate female strobili from outside pollen contamination, and a known pollen is applied at the time of maximum female strobilus receptivity. The goal of this study was to compare prototype pollination bags made by PBS International to the industry standard kraft paper pollination bag with and without a support wire for female strobili survival and to assess their efficiency for mass production of controlled cross loblolly pine seed. A multiyear study compared 13 pollination bag types at more than nine seed orchard sites across the southeastern United States. There were significant differences among bag types for conelet survival at the time of bag removal that persisted until cone harvest 18 months later. Female strobili bagged in prototype PBS-I2 were over three times more likely to survive to cone harvest than strobili inside the traditional kraft pollination bag. Two of the PBS bag types had the highest estimated filled seed per bag. One PBS bag was faster to install and remove than the kraft paper bag with a support wire.

Genetic parameters of Gill-associated virus infection and body weight under commercial conditions in black tiger shrimp, Penaeus monodon

Selective breeding to improve performance of growth and increase disease resistance is becoming commonplace within shrimp aquaculture. Whilst estimated breeding values (EBV) for growth can be evaluated easily in on-farm trials, EBVs for disease resistance are usually obtained from controlled laboratory challenges and may not be indicative of natural infection and resistance in a commercial setting. If they are not the same trait, this will result in a low genetic correlation between the traits and application of EBVs derived from the laboratory challenge will lead to overall slow genetic progress for improved disease resistance in on-farm conditions. There is a need for alternative measures of predicting disease resistance based on performance in farm environments. Two such estimates may be viral infection status (presence/absence) and load of farm reared shrimp.This study presents genetic parameter estimates of Gill-Associated Virus (GAV) infection (viral infection presence and viral loading) and body weight traits from Penaeus monodon reared under commercial farm conditions. Body weight and GAV infection traits were assessed by sampling ~2000 shrimp from 80 full-sib families from two replicate commercial ponds. In addition, the Pearson correlation of EBVs of pond-reared shrimp with those of siblings derived from communal laboratory GAV challenge tests (intramuscular injection of standard doses of virus) were calculated to establish if prediction of genetic merit in controlled trials would be similar to disease resistance seen on-farm.Heritability under commercial farm conditions for GAV infection status was 0.06 ± 0.03 (percent GAV positive 45.5%) and infection load 0.21 ± 0.10 (mean GAV infection load 3.11 ± 1.14 log10 GAV copies μg−1 TNA) and for body weight h2 = 0.38 ± 0.07. A high genetic correlation was observed among the two on-farm GAV infection traits (rg = 0.90 ± 0.24), whereas the genetic correlation between the two GAV infection traits and body weight on-farm were positive although weak (rg = 0.26 ± 0.25; 0.36 ± 0.26). No significant correlation was found for EBVs of GAV infection (infection status and load) on-farm and GAV-induced mortality or viral load under laboratory challenge testing (REBV ranged from −0.06 ± 0.14 to −0.27 ± 0.15). Additionally, there was no correlation of EBVs between body weight of shrimp on-farm and GAV-induced disease under controlled challenge. In conclusion, measures of GAV infection from shrimp on-farm and GAV induced mortality measured under controlled challenge conditions may represent different genetic traits, at least when mortality is measured using an ‘unnatural’ challenge method and when no apparent disease outbreak occurs on farm.

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus).

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 – 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program.

AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data.

SummaryAlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at <1x coverage.Availability and implementationAlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.Supplementary information Supplementary data are available at Bioinformatics online.

First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus).

Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96cM with an average marker interval of 0.33cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.

Screening and characterization of sex-specific markers developed by a simple NGS method in mandarin fish (Siniperca chuatsi)

Sex-specific markers are the prerequisite for interpreting the mechanisms of sex determination and sex control breeding in fish. Here, we provided a simple next generation sequencing strategy to identify potential sex-specific sequences in mandarin fish (Siniperca chuatsi) that is a greatly important freshwater fish in China. Through genome assembly, reads mapping, sequencing depth and coverage analysis of sequenced genomes of three males and three females, we identified 212 potential male-specific sequences. After two rounds of verification, a total of eight primer pairs were identified as potential candidate markers to be able to distinguish the genetic sex of mandarin fish. Subsequently, the best three markers were further tested in another four different farmed populations of mandarin fish, and the authenticity was 100%. Moreover, based on these markers, eight neomales were demonstrated to be genetic females and about 1: 1 sex ratio was observed in 215 juvenile offspring from two full-sib families. Notably, a duplicate of anti-Müllerian hormone, a gene participating in sex determination process in fish, was identified from the verified male-specific sequences. Overall, this study provided a simple and effective next generation sequencing method to identify sex-specific sequences and the male-specific molecular markers suggested an XY sex determination system in mandarin fish.

Adaptation potential of the copepod Eurytemora affinis to a future warmer Baltic Sea.

To predict effects of global change on zooplankton populations, it is important to understand how present species adapt to temperature and how they respond to stressors interacting with temperature. Here, we ask if the calanoid copepod Eurytemora affinis from the Baltic Sea can adapt to future climate warming. Populations were sampled at sites with different temperatures. Full sibling families were reared in the laboratory and used in two common garden experiments (a) populations crossed over three temperature treatments 12, 17, and 22.5°C and (b) populations crossed over temperature in interaction with salinity and algae of different food quality. Genetic correlations of the full siblings’ development time were not different from zero between 12°C and the two higher temperatures 17 and 22.5°C, but positively correlated between 17 and 22.5°C. Hence, a population at 12°C is unlikely to adapt to warmer temperature, while a population at ≥17°C can adapt to an even higher temperature, that is, 22.5°C. In agreement with the genetic correlations, the population from the warmest site of origin had comparably shorter development time at high temperature than the populations from colder sites, that is, a cogradient variation. The population with the shortest development time at 22.5°C had in comparison lower survival on low quality food, illustrating a cost of short development time. Our results suggest that populations from warmer environments can at present indirectly adapt to a future warmer Baltic Sea, whereas populations from colder areas show reduced adaptation potential to high temperatures, simply because they experience an environment that is too cold.