Traits In Landraces Research Articles

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Multivariate genome-wide associations for immune traits in two maternal pig lines

BackgroundImmune traits are considered to serve as potential biomarkers for pig’s health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines.ResultsIn total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified.ConclusionsThis study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.

Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change.

Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.

Yield and water-use related traits in landrace and new soybean cultivars in arid and semi-arid areas of China

Empirical soybean breeding has improved its yield in arid and semi-arid areas of China. The objective of this study was to identify the important traits found in successful commercial soybean cultivars following the domestication of landraces through breeding in the semi-arid region of North-west China. A further objective was to identify any key traits that can be targeted using trait-based selection to improve yield under drought. Seed yield, phenology, water-use, water-use efficiency and their related traits in soybean landraces and successful cultivars were compared over a four year period in the field and this was supplemented with an outdoor pot experiment. The results in both field and pot experiments showed that successful soybean cultivars have a reduced thermal time to flowering but the thermal time for seed filling has increased. This change in partitioning of phenological time in the commercial cultivars resulted in a lower number of pods, fewer seeds per unit area but an increase in 100-seed weight, harvest index and seed yield. New soybean cultivars with high seed yield also had a lower vegetative biomass and less water use in both field and pot experiments than landraces but the lower water use did not compromise seed yield. The commercial cultivars also had a lower pod wall ratio (ratio of pod wall weight to total pod weight at maturity) which also contributed to yield by improving harvest index. We conclude that the key traits that have been altered as a result of soybean breeding in arid and semi-arid areas of China have been (1) a shortening of the duration between sowing and flowering but an extension of the seed filling period, (2) fewer pods but an increase in seed number per pod and 100-seed weight and also a decreased pod wall ratio, (3) an increased harvest index and (4) a reduced water use, particularly in the deeper soil layers. • Yield improvements in soybean in dry areas were investigated in a study over four years. • Soybean breeding resulted in a shorter thermal time to flower but a longer thermal time for seed filling. • The longer reproductive period resulted in a higher seed number per pod, seed weight and seed yield. • A reduction in the thermal time to flowering reduced leaf fraction and total water-use but did not compromise seed yield. • Newer varieties had lower soil water use at depth but a higher HI than the landraces.

Genetic analysis of yield related traits in landrace × commercial watermelon hybrids

Watermelon [Citrullus lanatus var lanatus L.] is a major xerophytic crop originating in Africa especially grown in subtropical and tropical parts of the world. However, few adapted varieties are available to promote greater yield and make watermelon a viable commercial crop of choice. Path analysis and combining ability was carried out for yield related traits among three popular local landraces; Landrace1, Landrace 2 and Landrace 3 collected in Zimbabwe and three commercial watermelon varieties ‘Congo’, ‘Charleston Grey’ and ‘Crimson Sweet’ in plots arranged in an RCBD replicated 3 times. A complete diallel mating design was used to generate 36 F1 genotypes which together with the parents were evaluated for several quantitate traits. Data on correlations, path analysis, GCA and SCA between fruit yield and other traits were computed using Microsoft Excel and GenStat 17. Individual fruit weight (FIW) and the number of fruits per plant (NF) were found to be significantly linked with final fruit yield. Significant positive correlations were also observed on NF and number of female flowers (NFF), number of vines (NV), and FIW and these traits could be recommended as reliable selection indicators for creating high yielding watermelon genotypes. Path analysis showed that FIW and NF were the most important contributors to watermelon yield. GCA and SCA effects were significant and positive for yield which indicates that the traits are controlled by both additive and non-additive genes. ‘Crimson Sweet’ and ‘Landrace 1’ were the best pollen sources whereas ‘Landrace 1’ and ‘Landrace 2’ were the highest yielders when used as female parents. Overall, results from this study identified usable yield related proxies and need to incorporate local landraces germplasm in watermelon improvement.

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

127 Antibody Response as an Indicator Trait for Improved Reproductive Performance During a PRRSV Outbreak: Genetic Correlations of S/P Ratio with Reproductive Traits in Landrace and Duroc Sows

Abstract Previous studies proposed the use of antibody response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), measured as sample-to-positive (S/P) ratio, as a potential indicator trait to improve the reproductive performance of PRRSV-infected Landrace sows. However, this indicator trait has not yet been validated in Landrace sows or evaluated in a terminal sire line, such as Duroc. The main objective of this work was to perform host-genetic analyses of S/P ratio and reproductive traits during a PRRSV outbreak in maternal and terminal breeds. The data consisted of 690 Duroc and 541 Landrace multiparous sows (1.9±1.2 and 2.3±1.5, respectively) with S/P ratio collected at approximately 54 days after the predicted beginning of the outbreak. Of these, 644 Duroc and 528 Landrace sows also had reproductive data recorded during the PRRSV outbreak comprising number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NBM), number born dead (NBD; sum of NSB and NBM), total number born (TNB; sum of NBA and NBD), and number weaned (NW). All animals had genotype data on ~30K SNPs common across both breeds. Heritability estimates (± standard error) of S/P ratio during the PRRSV outbreak were moderate, with 0.33±0.06 for Duroc and 0.28±0.07 for Landrace. Reproductive traits during the PRRSV outbreak had overall low heritability estimates (≤0.18). Favorable genetic correlations of S/P ratio with NBA (0.65±0.33), in accordance with previous studies, and NBD (-0.33±0.28) were observed for Landrace sows only. Estimates of genetic correlation with other traits were -0.21±0.30 (NBM), -0.12±0.29 (NSB), 0.10±0.38 (NW), and 0.54±1.29 (TNB) for Landrace. For Duroc, these estimates were weaker: -0.33±0.40 (NBA), 0.26±0.27 (NBA), and 0.28±0.30 (NW), with convergence issues for mortality traits. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRSV outbreak in Landrace sows.

Discovery of beneficial haplotypes for complex traits in maize landraces

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.

Estimation of genetic parameters and breeding values for growth traits using random regression model in Landrace × desi crossbred pigs

The experiment was conducted to estimate genetic parameters and breeding value of pre-weaning and postweaning growth traits in Landrace × Desi (indigenous) crossbred pigs. Random regression model (RRM) with fixed effects, random effects of direct additive, maternal genetic, maternal permanent environmental and individual permanent environmental effects and a heterogeneous residual variance structure over growth measurement at different time point was applied to estimate the genetic parameters. Among different order of Legendre polynomial fitted, RRM with heterogeneous error variance (RRM–HET) with fourth order fit for direct genetic, maternal genetic and maternal permanent environmental effect and third order fit for individual permanent environmental effect was found as the best model. The direct genetic heritability estimates were 0.299±0.021 at birth, which was low (0.011±0.006) at W12 and high at W36 (0.582±0.03). The first eigenvalue accounted for more than 98% variation in body weight and the corresponding trajectories had positive values displaying almost linear pattern till weaning and then increased rapidly in post weaning age. This showed that the selection of pigs on the basis of mean body weight at early age can also result in higher body weight in post-weaning stages. The average breeding value for the birth weight, W8 and W32 was 0.951 kg, 10.162 kg and 49.598 kg, respectively. The 42.86% of sire population at W12 and 56.76% at W24 had breeding value higher than the population's mean breeding value indicating existence of genetic variation and thus the scope for increasing the selection pressure.

Microsatellite DNA Markers and Their Correlation with Body Traits in Landrace, Duroc and Henan Western Black Pigs

Twelve microsatellite loci were selected from the Food and Agriculture Organization of the United Nations to examine the genetic structure and relationship between microsatellite DNA and body traits including height, back height, body length, chest width, chest depth, head Length, Ear area, and forehead width. Twelve microsatellite loci analyzed were polymorphic in Landrace, Duroc and Henan Western Black Pigs. The total number of alleles found for the twelve microsatellite loci amounted to 150.The average expected heterozygositie ranged from 0.1287 to 0.8301 among twelve loci, and the average polymorphic information content ranged from 0.1168 to 0.7894. The results of cluster analysis showed that the genetic distance between Henan Western Black Pigs and Duroc was least 0.1414. Microsatellite loci of SW72 were significantly associated with back height and chest depth (plessthan0.05), while SO002 were significantly associated with chest depth and head Length (plessthan0.05). Finally, the results showed that Henan Western Black Pigs has a high level of genetic polymorphism and genetic differentiation. Cluster analysis shows that the relationship between Black Pigs and Duroc is closer. These were significantly associated with body traits in five microsatellite loci, including SW72, SO002, SW632, SO090 and SW1828 (plessthan0.05). These results provided scientific reference for the further cultivation and utilization of black pigs.

Diversity analysis and trait association study for antioxidants and quality traits in landraces, farmers’ varieties and commercial varieties of Indian short day garlic (Allium sativum L.)

Garlic (Allium sativum L.) is the second most important Allium crop throughout the world, used raw, cooked, processed or an ingredient of traditional and modern medicine. It is one of the richest sources of total phenolics among the usually consumed vegetables. Indian garlic is indispensable item of globally famous and savoured traditional Indian cuisine. The genotypes grown are mostly short-day type, soft-neck with greater storage ability. Apart from dry bulbs, green garlic leaves are widely consumed in India. In the absence of sexual mode of reproduction, the development of new varieties is limited compared to other Alliums and breeding effort is focused on selection of elite clones from the available genetic resources. The aim of the present study was to (1) study the variations for antioxidants and antioxidant activities in leaf and clove samples of different accessions and (2) study the trait association and diversity in the collection for further selection. Antioxidant compounds were higher in cloves while green leaves were superior for antioxidant activity with variations in few lines. Commercial variety G-323 was found superior for leaf antioxidant activity and clove antioxidant content. Farmers’ variety scored higher for total soluble solids while breeding lines scored better for pungency. Total soluble solids and pungency mostly had negative association with antioxidant compounds and antioxidant activity. The diversity was independent of geographic region and status of selection (varieties, landraces and farmers’ varieties). The quality trait improvement effort should focus on medium TSS and pungent varieties for greater health benefits.

68 Genomic prediction accuracies of vulva size traits in Landrace and Yorkshire gilts

Abstract Recent results indicated that vulva size measured prior to puberty may be predictive of reproductive performance in sows. Therefore, the objective of this study was to estimate genomic prediction accuracies for vulva size traits in purebred gilts. A total of 1,185 Landrace (n = 477) and Yorkshire (n = 708) gilts originated from two different lines were used in this study. All animals had vulva size measurements taken at an average 21.5 weeks of age (SD = 5.8). Measurements included vulva width (VW), vulva height (VH), and vulva area (VA). Genotype data (Geneseek GGP-HD) was available for all animals, for ~40K SNPs. Marker allele substitution effects were estimated using Bayes-B (pi = 0.99) in a model including the fixed effects of contemporary group, line, breed (for multi-breed analysis only) and body weight (covariate), and the random effect of SNPs. Genomic prediction accuracies were estimated using three training and validation strategies: between-breed, within-breed (4 and 6 cross-validation folds for Landrace and Yorkshire, respectively), and multi-breed (10-fold cross-validation, using one-fold per breed for validation at a time). Between-breed accuracies were low and consistently negative, with -0.02, -0.10, and -0.05 in Landrace and -0.05, -0.04 and -0.03 in Yorkshire, for VW, VH, and VA, respectively. Within Landrace, these were moderate, with 0.35 (VW), 0.42 (VH), and 0.56 (VA), whereas lower accuracies were obtained for Yorkshire, with 0.07 (VW), 0.20 (VH), and 0.14 (VA). Multi-breed accuracies were low with 0.14 (VW), 0.14 (VH), and 0.24 (VA) for Landrace, and 0.03 (VW), 0.16 (VH), and 0.09 (VA) for Yorkshire. These results indicate that genomic selection for vulva size traits is possible in Landrace, but limited in Yorkshire gilts. The low between- and multi-breed results suggest that QTL for these traits are in opposite phases between breeds and/or do not segregate in both breeds. Financial support from the Iowa Pork Industry Center is appreciated.

Unravelling the relationship between adaptation pattern and yield formation strategies in Mediterranean durum wheat landraces

Abstract Understanding the environmental and genetic factors behind the adaptation of landraces to different environments may help design breeding strategies and to promote yield improvement. Based on previous results that showed a differential frequency of alleles associated with important agronomic traits in landraces that originated in the east (EM) and the west (WM) of the Mediterranean Basin, this study analysed their patterns of adaptation and the influence this adaptation has on yield formation strategies. Thirteen and thirty-one genotypes selected according to their membership coefficient (q>0.900) from the EM and the WM genetic subpopulations, respectively, were tested during six crop seasons under rainfed Mediterranean conditions. Yearly yields ranged from 3173 to 4917 kg/ha. EM landraces showed more spikes per unit area, while WM ones showed consistently taller plants, larger cycle length to anthesis, a shorter grain filling period, a higher grain filling rate and heavier grains. The contrasting pattern of adaptation of the two subpopulations was based on a differential ability to use the water available before and after anthesis. The yield of EM landraces, originated in the warmest and driest area of the Mediterranean basin, relied mostly on water input before anthesis, which was beneficial for spike production and for the accumulation of water-soluble carbohydrates in the stems prior to anthesis, to be remobilized to grains during grain filling. WM landraces performed better in environments with high water input during grain filling, which was efficiently used to increase grain setting and produce heavy grains. EM landraces could be used in breeding to improve the adaptation of modern varieties to terminal drought.

Physiological characterization of common bean (Phaseolus vulgaris L.) under abiotic stresses for breeding purposes.

In the Brazilian wet and dry seasons, common beans (Phaseolus vulgaris L.) are grown under rainfed conditions with unexpected episodes of drought and high temperatures. The objective of this study was to evaluate the physiological mechanisms associated with drought adaptation traits in landraces and line/cultivars of beans from the Andean and Mesoamerican gene pools. Twenty-five genotypes, contrasting in terms of drought tolerance, were evaluated in a phenotyping platform under irrigated and rainfed conditions. Agronomic and physiological parameters such as grain yield, shoot structures, gas exchange, water potential, and osmotic adjustment were evaluated. The stress intensity was estimated to be 0.57, and the grain yield reduction ranged from 22 to 89%. Seven accessions, representative of the Andean and Mesoamerican germplasm (CF 200012, CF 240056, CF 250002, CF 900004, CNF 4497, CNF 7382, and SEA 5), presented superior performance in grain yield with and without stresses. The physiological responses under abiotic stresses were highly variable among the genotypes, and two Mesoamerican accessions (CF 200012 and SEA 5) showed more favorable adaptive responses. As the main secondary physiological traits, gas exchange and osmotic adjustment should be evaluated together with the grain yield to increase the selection efficiency of abiotic stresses-tolerant common bean lines.

Genetic parameters and trends for production traits and their relationship with litter traits in Landrace and Yorkshire pigs.

Genetic parameters and trends in the average daily gain (ADG), backfat thickness (BF), loin muscle area (LMA), lean percentage (LP), and age at 90kg (D90) were estimated for populations of Landrace and Yorkshire pigs. Additionally, the correlations between these production traits and litter traits were estimated. Litter traits included total born (TB) and number born alive (NBA). The data used for this study were obtained from eight farms during 1999 to 2016. Analyses were carried out with a multivariate animal model to estimate genetic parameters for production traits while bivariate analyses were performed to estimate the correlations between production and litter traits. The heritability estimates were 0.52 and 0.43 for ADG; 0.54 and 0.45 for BF; 0.25 and 0.26 for LMA; 0.54 and 0.48 for LP; and 0.56 and 0.46 for D90 in the Landrace and Yorkshire breeds, respectively. The ADG and D90 showed low genetic correlation with BF and LP. The LMA had -0.40, -0.32, 0.49, and 0.39 genetic correlations with ADG, BF, LP, and D90, respectively. Genetic correlations between production and litter traits were generally low, except for the correlations between LMA and TB (-0.23) in Landrace and ADG and TB (-0.16), ADG and NBA (-0.18), D90 and TB (0.19), and D90 and NBA (0.20) in Yorkshire. Genetic trends in production traits were all favorable except for LMA.

The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study.

ObjectiveThe purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs.MethodsThe traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records.ResultsThe outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL.ConclusionThe genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

Genetic Diversity Assessment of Quantitative Traits in Landraces of Aus Rice

Genetic diversity of 46 landraces of Aus rice was studiedunder irrigated condition through Mahalanobis D2 statistics for grain yield and yield contributing characters. The genotypes were grouped into seven clusters. The highest inter-genotype distance was observed between the genotypes Lalgalong and Langrabeni and the lowest between Saita and Korchamuri respectively. The intra cluster distances were low for all the clusters ranging from 0.64 in cluster IV to 1.17 in cluster I. The highest inter cluster value was 11.45 (between cluster III and V) and the lowest was 4.36 (between cluster VI and VII). The highest cluster means for effective tiller number and grain yield per hill were obtained from cluster III. On the other hand, the highest leaf width and the highest spikelet fertility from cluster IV, tallest plant and the highest grain breadth from cluster VI, the highest 1000-grain weight from cluster V whereas the lowest mean value for days to 50% flowering and days to maturity were found in cluster VI.The genotypes from cluster III could be hybridized with the genotypes of other clusters for producing transgressivesegregants. Canonicalvectoranalysis revealed that days to 50% flowering and days to maturity were contributed maximum to the genetic divergence. Principal Coordinate Analysis (PCoA) revealed that the genotypes Begun bitchi, Rang mahal, Laxmijhota, Katar, Chiknal, Manikmendal, Baismugurwere found far away from the centroid of the cluster and can be selected as parents for further breeding programs.The results suggested thatLalgalong (acc. no. 1655) and Langrabeni (acc. no. 1645) can be crossed with the genotypes of cluster III and cluster VI to develop more promising as well as high yielding variety for Aus season.

Analysis of the associations between polymorphisms in GNAS complex locus and growth, carcass and meat quality traits in pigs

Imprinted genes are interesting candidates for marker assisted selection in farm animals. One of them-GNAS complex locus is engaged in obesity pathogenesis in humans and mice. In our study, we identified new polymorphism in porcine GNAS gene (variable number of CT repeats, accession number: rs196952953) and found that this polymorphism is in linkage disequilibrum with GNAS AM490165:g.324C>T. Statistical analysis (GLM procedure), performed on 552 animals (Large White n = 258 and Landrace n = 269), revealed that deduced haplotypes and GNAS AM490165:g.324C>T are associated with growth performance and a few carcass traits, but not with feed intake. We observed significant additive effects of GNAS AM490165:g.324C>T genotype and haplotype 2 (C/278 bp) on test daily gain (TDG), average daily gain (ADG), number of days on test, age of the slaughter (P < 0.01) and FCR ratio (P < 0.05). Animals with two copies of C/278 haplotype had significantly higher: TDG, ADG, lower feed:gain ratio and faster reached the weight of 100 kg. When carcass traits were considered, significant associations between GNAS AM490165:g.324C>T polymorphism, haplotype 2 (C/278) and weight of ham with and without backfat and skin (WH) (WH2), length of the carcass, height and the width of the loin, meat percentage, weight of the main cuts were identified. The significant dominance effects of GNAS AM490165:g.324C>T polymorphism and haplotype 2 on WH and WH2 were observed (P < 0.05). When the two breeds were analyzed separately significant associations were observed for most of the traits in Landrace while in Large White the same trends were present but the differences were mostly not significant. Among meat quality traits we found significant association between haplotype and IMF content in Landrace (P < 0.03). Our results show for the first time that GNAS complex locus may modulate economically important traits in pigs.

Expression patterns of insulin-like growth factor system members and their correlations with growth and carcass traits in Landrace and Lantang pigs during postnatal development

The IGF system plays important roles in growth. Nevertheless, few data have been reported so far on the expression of IGF system members and their relationship with growth in domestic animals, especially pigs. In this study, hepatic transcript level of IGF1, IGF2, IGF binding protein 2 (IGFBP2), IGFBP3 and IGF 1 receptor (IGF1R), plasma protein level of IGF1 and IGFBP3, and eight growth or carcass traits, including chest circumference, body length, body height (BH), body weight, carcass weight, loin muscle area (LMA), back fat thickness and average daily gain, were measured in fast-growing Landrace and slow-growing Lantang pigs at the age of 1, 27, 90, 150 and 180 days. The results showed that liver mRNA level of IGF1, IGF2 and IGF1R, and blood protein level of IGF1 have a similar developmental profile in both Landrace and Lantang pigs. Their levels were higher at the early age than that at other older ages. Hepatic transcript abundances of the two growth inhibitors, IGFBP2 and IGFBP3, were mostly higher in Lantang pigs than that in Landrace pigs, at 5 examined postnatal stages. The IGF system members' liver mRNA level and/or serum protein level have significant correlation with each other in different age of Landrace or Lantang pigs. Hepatic mRNA level or serum protein level of IGF system members also has significant correlation with investigated traits, especially with BH and LMA, in different age of Lantang or Landrace pigs. Our results revealed the change profiles of porcine IGF system members' liver transcript level and plasma protein level between different pig breeds and different postnatal developmental ages. Moreover, the correlation analysis results suggest that the IGF system members act coordinately to regulate the growth performance and carcass composition in pigs. The information obtained from the present study is important for elucidation of the regulatory mechanism of IGF system underlying growth, and for genetic improvement in pigs.

Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace × Chinese‐European crossbred population

Several quantitative trait loci (QTL) for different meat quality traits have been localized on the q arm of porcine chromosome 2 at position 55-78 cM. Association analyses were performed in a commercial Landrace × Chinese-European (LCE) crossbred population (n = 446) slaughtered at approximately 127 kg and an average age of 198 days with records for performance (growth, fat and meat accretion) and meat quality [intramuscular fat (IMF), Minolta L*, Minolta a*, Minolta b* and pH at 45 m]. Polymorphisms within positional candidate genes cloned from homologous regions on human chromosome 19, ubiquitin-like 5 (UBL5- AM950288:g.566G>A), resistin (RETN- AM157180:g.1473A>G causing substitution p.Ala36Thr), insulin receptor (INSR- AM950289:g.589T>C) and complement factor D (adipsin) (CFD- AM950287:g. 306C>T) were located at positions 62.1, 64.0, 68.0 and 70.7 cM respectively on the current USDA USMARC map of porcine chromosome 2 and had the following allele frequencies in the LCE: UBL5 566G - 0.57; RETN 1473G - 0.84; INSR 589C - 0.70; and CFD 306C - 0.73. The effects of alleles within the candidate genes on the recorded traits were estimated using an animal model. Significant effects (P < 0.05) were found for pH(45) in m. semimembranosus (m. sm.) (UBL5), IMF (RETN) and Minolta L* (RETN, CFD). Differences between phenotypic means of homozygotes at UBL5, RETN and either RETN or CFD explained 0.34 SD for pH(45) in m. sm., 0.47 SD for IMF and 0.68 SD for Minolta L* respectively. Suggestive effects (P < 0.10) on IMF (UBL5, CFD), Minolta a* (INSR, CFD) and Minolta b* (INSR) were also observed. Our results support the localization of further QTL for meat quality traits in this region and suggest that there are several genes affecting different meat quality traits.