Commercial Breeding Programs Research Articles

Differential family-based survival of Pacific White shrimp during communal larval culture and implications for selective breeding programs

Differential larval survival of Penaeid shrimp families when reared communally for any of the mainstream species is widely acknowledged as a likely scenario commercially. However, no scientific data exist in the public domain that quantifies the magnitude of this phenomenon. We report on the differential survival of Pacific White shrimp, Litopenaeus vannamei, families when reared communally during commercial larval rearing and provide explanations of the impacts of such occurrences on managing commercial selective breeding programs. In total 76 families are pooled in two groups of 40 and 36 families and reared through to PL15/16, respectively. DNA microsatellite markers were then used to assign PL15/16 to their family of origin, and the abundance of PL in each family was used to calculate survival rates at a family-based level during commercial communal larval rearing. Calculated survival distributions of 76 families during the larval culture phase ranged from 0 to 100 % with three of the 76 families having no survivors present at PL15/16. Despite all families being stocked into larval culture with somewhat equal representation, only 18 of the 76 families made up 50 % of the population at PL15/16 that would then be stocked into ponds. We found no correlation between the number of nauplii produced per spawning (family) versus the calculated number of PL15/16 alive after the larval rearing phase. Together these three factors have significant implications in Penaeid shrimp selective breeding programs. If populations are not managed appropriately, there is a risk of significant reduction in a programs’ effective population size.

A FIRST PEDIGREE-BASED ANALYSIS (PBA) APPROACH FOR THE DISSECTION OF DISEASE RESISTANCE TRAITS IN GRAPEVINE HYBRIDS

To date, molecular markers are available for many economically important traits in grapevine (Vitis vinifera L.) as well as in other fruit crops. Unfortunately, lack of knowledge of the allelic variation of the related genes hampers their full exploitation in commercial breeding programs. These markers have usually been identified in a single cross. Consequently, only one or two favourable alleles of the related quantitative trait loci (QTL) are identified and exploitable for marker-assisted breeding (MAB), whereas a breeding program may include several alleles. Our novel employed approach, namely pedigree-based analysis (PBA), allows for the identification and exploitation of most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus covering multiple generations and linking many crosses through their common ancestors in the pedigree. In this study we focus on the genetic characterization of numerous Vitis hybrids, donors of resistance to downy and/or powdery mildew, in order to identify selection signatures. In particular, 120 hybrids of American origin and 100 European hybrids, along with 44 related V. vinifera cultivars, have been genotyped at 190 SSR loci. These markers have been chosen based on their physical distance in order to have 10 SSRs well-scattered along each chromosome. Based on the SSR profiles, the historical pedigree records have been verified. Following the trueness-to-type validation for most of the studied hybrids, the identity-by-descent (IBD) analysis has been performed, tracing the allelic flow through the successive generations. Here we report results about the identification of non-vinifera genomic intervals retained into the vinifera background and the anchoring of the discovered breeding signatures to the grapevine genome. In addition, we report on the PBA-based QTL results for segregating populations coming from pedigree-supported parental genotypes donors of resistance to downy mildew in north-eastern Italy.

Genetic and Environmental Variation in a Commercial Breeding Program of Perennial Ryegrass

ABSTRACTImplementation of genomic selection (GS) for the genetic improvement of forage crops, such as perennial ryegrass, requires the establishment of sufficiently large training populations with high‐quality phenotype and genotype data. This paper presents estimates of genetic and environmental variance and covariance components, obtained in a training population of 1453 F2 families. These families were produced in 2001, 2003, 2005, and 2007, and they were tested at seven locations throughout Europe. Families were cultivated together with commercial varieties that were used as control. Analyses focused on forage yield (green and dry matter) and six traits scored by visual inspection (i.e., rust resistance, aftermath heading, spring growth, density, winter hardiness, and heading date). Data were analyzed with linear mixed models, including fixed effects (trial and control varieties, within year and location), and random effects (breeding values, pedigree or parents, repeated effects of family or parents within location, and within trial environmental effects, to recover interblock information). Results showed very significant genetic variances for all traits, which provide good opportunities for future GS‐based breeding programs. Forage yield showed family heritabilities of up to 0.30 across locations and up to 0.60 within a location. Similar or moderately lower values were found for the other traits. In particular, the heritabilities of rust resistance and aftermath heading were very promising. Genetic correlations between traits were generally low but positive, which increases the potential for multitrait selection.

Identification of quantitative trait loci for bolting and flowering times in Chinese kale (Brassica oleracea var. alboglabra) based on SSR and SRAP markers

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR), simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers were used to construct the first intra-specific genetic linkage map for B. oleracea var. alboglabra. In addition, QTL locations were determined for bolting and flowering traits. A total of 189 polymorphic marker loci were detected in the two parents, with 45 marker loci not located on any linkage group (LG). The remaining 144 loci defined ten LGs and included 69 EST-SSR loci, three SSR loci, and 72 SRAP loci. The length of the map was 1,173.8 cM, the average distance between loci was 8.15 cM, and the proportion of segregation distortion loci was 25.7%. Three QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2:3 generation, which explained 37.07% and 18.44% of the phenotypic variation, respectively. Two QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2 generation, which explained 27.90% and 25.59% of the phenotypic variation, respectively. In both generations, QTLs ftB.1 and ftA.1 were located on LG5, and the distance between the two QTLs was only 1.0 cM, suggesting that they could be at an identical locus. These results provide a useful reference for future QTL studies on bolting and flowering time in B. oleracea var. alboglabra, and can be used to identify markers linked to these QTLs for marker-assisted selection in commercial breeding programmes.

Of growing importance: combining greater early vigour and transpiration efficiency for wheat in variable rainfed environments.

Increasing climate variability, particularly variability in the timing and amount of soil water, means that breeding wheat (Triticum aestivum L.) varieties with stable high grain yields is increasingly more challenging. Changing environmental conditions in water-limited rainfed environments will alter genotype ranking to reduce confidence in the identification of consistently higher yielding performers. Greater early vigour (EV) and transpiration efficiency (TE) are two physiological traits that have demonstrated benefits as breeding targets for efficient water-use in Mediterranean in-season water and monsoonal stored water environments, respectively. This Perspective discusses the hypothesis that combining higher TE and greater EV will broaden the adaptation and increase grain yields for wheats grown across most rainfed environments. We examine the physiology underpinning adaptation with greater EV and higher TE, as well as the challenges and potential benefits of deploying these traits in combination. We then discuss how these two traits interact with different environments and, in particular, the different wheat-growing regions of Australia. We conclude that the combination of these two traits is genetically and physiologically feasible, as well theoretically beneficial to average yield in most rainfed environments. Hence, we suggest a strategy for reliably managing the complex genetics underpinning EV and TE when phenotyping and selecting both traits in commercial wheat breeding programs.

From Ideotypes to Genotypes: Approaches to Adapt Wheat Phenology to Climate Change

IntroductionSimulations using crop models can assist in designing ideotypes for current and future agricultural conditions. This approach has been often in recent years to identify avenues for adapting wheat to climate change. However, this approach has rarely been used to guide commercial breeding programs. We hypothesize that the lack of link between models and the available tools for breeding, i.e. available genetic variability and selection methods. Materials and methods- We use a modified ARCWHEAT2 phenology model and future climate data from the ARPEGE global circulation model to identify targets for future phenologies-We genotyped over 400 French cultivars for known phenology genes and confronted the genetic make-up of these varieties to their success in France over the past 25 years- We developed a methodology to link model parameters to underlying marker data. We tested the performance of the methodology against circa 60 varieties ResultsEarlier phenology may be an avenue for stress avoidance in the future.Current photoperiod sensitivity of early cultivars already poses problems in terms of adaptation, as exemplified by the interaction between Ppd-D1 and Vrn-A3We show that a gene-based model can be used to predict wheat phenology without a significant loss in predictive performance. DiscussionAnalyzing current phenology genes of existing cultivars and their adaptation allowed us to identify a limit to past breeding efforts in obtaining early cultivars. This requires that a more knowledge based approach be taken. Gene-based modelling of phenology is possible on a collection of elite, adapted varieties and provides the tools for constructing genotypes with specific allelic combinations leading to more appropriate constructions of earliness.

A study of heterosis, combining ability and heritability between two male sterile lines and ten inbred lines of Tagetes patula

Two male sterile lines (Ms-1, Ms-2) and ten inbred lines (K3, K4, K5, K8, K13, K15, K17, K20, K30, K33) were crossed according to Comstock and Robinson’s (in: Gowen (ed.) Heterosis, 1952) North Carolina Design II to estimate heterosis, combining ability, heritability and the phenotypic correlation coefficient for 11 ornamental characteristics of Tagetes patula. Twenty cross combinations and 12 parents were evaluated for 11 ornamental characteristics, in a randomized complete block design with three replications, in trials conducted during 2011 and 2012 at Huazhong Agricultural University, Wuhan, China. The results showed that the hybrid combinations displayed higher ornamental values and showed obvious heterosis over the male-parent for most of the ornamental traits evaluated. The male sterile line Ms-1 scored highly for general combining ability (GCA) with respect to the development of F1 offspring with a dwarf and compact plant habit, abundant double petals, and extended period between the opening and wilting of individual inflorescences. The male sterile line Ms-2 scored highly for GCA with respect to the development of F1 offspring with a large plant form and large flower size, as well as abundant flower numbers. The specific combining ability (SCA) of cross Ms-2 × K20 was found to be high, with progeny showing high positive heterosis over the male parent and superior mean values for all ornamental traits, thereby indicating that this cross has the potential to function as a superior cultivar within commercial breeding programmes. Both GCA effects and SCA effects were found to be important for the performance of individual hybrid combinations, and no clear relationship between GCA and SCA was found for these T. patula lines. The ratio of \(\sigma_{\text{GCA}}^{2} /\sigma_{\text{SCA}}^{2}\) for individual characteristics revealed that the relative importance of GCA and SCA to progeny quality varied for different traits. Estimates of heritability showed that many of the quantitative ornamental traits of T. patula were highly heritable, and the traits of diameter of center disk and number of ray florets should readily be improved by selection. By contrast, environmental factors influenced markedly on the traits of plant height, crown size, number of days between opening and wilting of inflorescences and the maximum number of flowers present each day. Phenotypic correlation coefficient analysis showed that the various vegetative growth characteristics were closely related to one another and, more interestingly, significant phenotypic correlations were found between the growth of the vegetative and reproductive structures of T. patula.

Physicochemical characterization of fruit quality traits in a German sour cherry collection

Several commercially relevant physicochemical fruit characteristics (fruit weight, fruit firmness, juice color intensity, soluble solid content, titratable acidity) were studied for three years during the research period 2005–2009 in 78 sour cherry genotypes of the Fruit genebank of the Julius Kühn-Institut in Dresden, Germany.A high phenotypic variability with significant differences between cultivars has been found for each of the fruit quality traits studied. Dependent on the trait, a certain number of cultivars were observed that showed lower or higher values than the commercially grown cultivars involved in this study. The favorable characteristics of a number of cultivars were consolidated by lower-year-by year variations in comparison to those of some commercial cultivars. The diversity of the physicochemical traits in the germplasm evaluated represents a basis for the selective choice of genotypes for commercial growing and breeding programs.

A New Race of Verticillium dahliae Causing Leaf Mottle of Sunflower in Europe.

Sunflower (Helianthus annuus L.) plants with symptoms of interveinal chlorosis were observed in the summer of 2013 in one field in Cadiz (Spain) where the performance of 30 hybrids was assessed. Symptoms affected 80% of the hybrids with incidence as high as 90%. Chlorosis and yellowing near the leaf margin were visible at floral initiation, and they progressed from the lower to upper leaves. Mottled leaves were observed near the top of the plants. On severely affected leaves, chlorotic patches enlarged, coalesced, and large areas of the leaves became necrotic and dried. Cross sections of the lower stem showed a brown discoloration of the vascular system. The fungus that was consistently isolated from stem and petiole tissues of sunflower plants was morphologically identified as Verticillium dahliae Kleb. (Vd) (5) and molecularly confirmed by PCR amplification of the 526-bp band (4). The race of the isolates was determined in a greenhouse experiment at 18 to 28°C from February to April 2014. Isolates 1-13 and 2-13 of Vd, obtained from two of the hybrids in 2013, one of them being Transol, were independently inoculated to 1-month-old plants of each of three sunflower genotypes: the susceptible hybrid Transol and the inbred lines HA89 (carrying the V1 gene for resistance to Vd) (2) and HAR5 (resistant to other diseases but with unknown reaction to Vd). Plants were inoculated by immersing roots in a suspension of 106 conidia per ml for 30 min. Inoculated plants were individually transplanted to 1-liter pots filled with sand/silt. Roots of the control treatments were immersed in water. Six replications (pots) were established for each isolate × genotype combination, according to a complete randomized 3 × 3 factorial design. Five weeks after inoculation, symptoms developed in 100% of the plants in the three sunflower genotypes. Severity of symptoms (SS) in each plant was assessed as percentage of foliar tissue affected. Significantly higher SS occurred on inoculated plants as compared to non-inoculated plants, which did not develop symptoms. Mean disease severity on inoculated plants was 80% (averaged across isolates and genotypes). A significant effect of genotypes was obtained. Mean SS averaged across isolates were 98, 73, and 69% for HAR5, HA89, and Transol, respectively. When stem tissues from the three sunflower genotypes were sampled and incubated on potato dextrose agar at 25°C, the mycelial growth of Vd was confirmed for the inoculated plants but not for the control plants. Isolates of Vd infecting the resistant inbred line HA89 have only been identified in Argentina (1) and the United States (3). To our knowledge, this is the first report of a race overcoming the V1 gene in HA89 in Europe. This poses a risk to commercial sunflower breeding programs in European countries.

Development of diagnostic markers for selection of the subacid trait in peach

Peaches with low acidity are preferred in the market and this trait is usually selected in commercial breeding programs. A major gene (D/d) has been described for this character located on linkage group 5 of peach, where the low acid character is determined by the dominant D allele. In this paper, we analyze a collection of 231 varieties and 542 offspring to identify diagnostic markers for this character. The CPPCT040 single sequence repeat (SSR) is known to be tightly linked to D. We found that one of its alleles (193) is diagnostic for the subacid character and identified with high probability individuals with low acidity (titratable acidity 24 kb) around CPPCT040, a region with higher than average SNPs between acid and subacid varieties. The CPPCT040 marker plus one of the SNPs identified (DH875) were used to genotype a collection of 542 seedlings, from different crosses expected to segregate for this character, which were phenotyped by tasting the fruit in the field. Data provided by both markers were always consistent and only 24 plants (4 %) did not fit the expectations. These markers and others that can be obtained from the haplotype identified can be readily used for marker-assisted selection in peach breeding.

Genetic differences between broodstock and offspring of seven-band grouper in a hatchery

The seven-band grouper (Epinephelus septemfasciatus) is an important fishery resource of a target for prospective aquaculture diversification and maintenance of stock quality is thus important. To explore the sustainability of fry production, genetic variations in 83 seven-band groupers from two broodstock and offspring populations of a hatchery strain were analyzed using 13 polymorphic nuclear microsatellite DNA loci; 133 alleles were identified. Allelic variability ranged from 4 to 18 in the broodstock and from 3 to 11 in the offspring. The average observed and expected heterozygosities were 0.669 and 0.734 in broodstock and 0.674 and 0.649 in offspring, respectively. Although no statistically significant reductions in heterozygosity or allelic diversity were evident in offspring, considerable loss of rare alleles was apparent. The broodstock and offspring populations exhibited significant genetic differences (F ST = 0.033, P < 0.001) indicating that genetic drift has likely promoted differentiation between the two populations, which may have negative effects on sustainable fry production. Therefore, genetic variations between broodstock and offspring should be monitored, and inbreeding should be controlled, to ensure the success of commercial breeding programs. Our data provide a useful genetic basis for future planning of sustainable culture and management of E. septemfasciatus in fisheries.

Phytochemical diversity of the essential oils of Mexican Oregano (Lippia graveolens Kunth) populations along an Edapho-climatic gradient.

Mexican oregano (Lippia graveolens) is an important aromatic plant, mainly used as flavoring and usually harvested from non-cultivated populations. Mexican oregano essential oil showed important variation in the essential-oil yield and composition. The composition of the essential oils extracted by hydrodistillation from 14 wild populations of L. graveolens growing along an edaphoclimatic gradient was evaluated. Characterization of the oils by GC-FID and GC/MS analyses allowed the identification of 70 components, which accounted for 89-99% of the total oil composition. Principal component and hierarchical cluster analyses divided the essential oils into three distinct groups with contrasting oil compositions, viz., two phenolic chemotypes, with either carvacrol (C) or thymol (T) as dominant compounds (contents >75% of the total oil composition), and a non-phenolic chemotype (S) dominated by oxygenated sesquiterpenes. While Chemotype C was associated with semi-arid climate and shallower and rockier soils, Chemotype T was found for plants growing under less arid conditions and in deeper soils. The plants showing Chemotype S were more abundant in subhumid climate. High-oil-yield individuals (>3%) were identified, which additionally presented high percentages of either carvacrol or thymol; these individuals are of interest, as they could be used as parental material for scientific and commercial breeding programs.

Tenualexin, Other Phytoalexins and Indole Glucosinolates from Wild Cruciferous Species

In general, the chemodiversity of phytoalexins, elicited metabolites involved in plant defense mechanisms against microbial pathogens, correlates with the biodiversity of their sources. In this work, the phytoalexins produced by four wild cruciferous species (Brassica tournefortii, Crambe abyssinica (crambe), Diplotaxis tenuifolia (sand rocket), and Diplotaxis tenuisiliqua (wall rocket)) were identified and quantified by HPLC with photodioarray and electrospray mass detectors. In addition, the production of indole glucosinolates, biosynthetic precursors of cruciferous phytoalexins, was evaluated. Tenualexin, (=2-(1,4-dimethoxy-1H-indol-3-yl)acetonitrile), the first cruciferous phytoalexin containing two MeO substituents in the indole ring, was isolated from D. tenuisiliqua, synthesized, and evaluated for antifungal activity. The phytoalexins cyclobrassinin and spirobrassinin were detected in B. tournefortii and C. abyssinica, whereas rutalexin and 4-methoxybrassinin were only found in B. tournefortii. D. tenuifolia, and D. tenuisiliqua produced 2-(1H-indol-3-yl)acetonitriles as phytoalexins. Because tenualexin appears to be one of the broad-range antifungals occurring in crucifers, it is suggested that D. tenuisiliqua may have disease resistance traits important to be incorporated in commercial breeding programs.

Assessment of parental contribution and effective population size from a 3×3 diallel cross of clam Meretrix meretrix

Unbalanced parental contribution and small effective population size (N (e)) are common issues during the artificial breeding of marine bivalves. The impact of hatchery-spawning practices on parental contribution, effective population size, the N (e)/N ratio, and genetic diversity are largely unknown. To address this, we conducted a parentage analysis on a complete 3x3 diallel cross of clam M eretrix meretrix using eight microsatellite markers. The genetic diversity of the parents was higher than that of their respective offspring in most crosses (8/9). Sires or dams from the same family contributed unequally to the pool of offspring from a particular cross, and the same parent clam exhibited large variation in parental contribution among different crosses. The variance in male contribution was higher than that of the female contribution in most crosses, suggesting that male contribution was more skewed than for females. The N (e)/N ratio for nine crosses ranged from 0.58 to 0.86. There was no linear relationship between the sex ratio and the N (e)/N ratio (P > 0.05). Moreover, a sex ratio closer to one-to-one does not necessarily mean a larger effective population size. A solution to small effective population size in commercial breeding programs is increasing broodstock numbers and attempting to maintain a balanced sex ratio.

The value of resequence data for poultry breeding: A primary layer breeder perspective

Poultry breeding companies are facing a new paradigm. Since 2004, extensive resources have been developed to increase understanding of the fundamental biology of the chicken. The chicken genome has been sequenced and revised twice, millions of novel DNA variants have been identified, and new tools have been created that allow rapid and inexpensive detection of these DNA variations. These developments have led to the establishment of molecular-based breeding programs within major poultry breeding companies that are revolutionizing the primary poultry breeding industries. Costs of sequencing continue to drop and are predicted to eventually reach the point where it is feasible to sequence the entire genome of elite birds before selection. There are multiple challenges to be resolved before this information can be fully incorporated into a breeding program. These include handling and analyzing the extremely large data sets generated, understanding which genes, variants, or both are relevant for commercial production traits, development of new bio-informatic tools, and integration of molecular information with traditional breeding programs. The novel variation identified within elite commercial lines will lead to enhancements in commercial breeding programs. Applications of this information include whole genomic selection, parentage identification, trait association studies, and quality control.

English

Genetic transformation is a widely employed tool in both basic research and commercial plant breeding programs. Its application requires that transgenes be stably integrated and expressed in the plant genome. When transgenic plants are developed, it is essential to determine which plants contain the transgene. Detection methods are usually based on amplification of the target transgene. This paper describes a development of detection method based on conventional and real time polymerase chain reaction (PCR) for simultaneous detection of barley HVA1 transgene and its transcript in transformed durum wheat. Since there exist a high homology between the barley HVA1 gene and the wheat gene, development of a specific sets of primers is needed for PCR-based characterizations, and the study of the transgene. Based on the alignment of the two genes sequences obtained from public databases, several primers were designed to detect and distinguish between the transformed and non-transformed plants. Real time PCR has been employed because of its inherent sensitivity and quantitative nature. It has been possible to design the following primers pairs F2/MMR, F2/R10 and F14/R10 as highly specific and suitable for the detection of HVA1 DNA by conventional and real-time PCR. Nonetheless, the primers used were allowed to reach high efficiencies and did not show any cross-reactivity with DNAs extracted from various plants. The sensitivity achieved was 6.4 pg. The primer pair F2/R10 was considered as highly specific for the detection of both DNA and mRNA of the HVA1 by real-time PCR. The assays proved to be accurate, specific, sensitive and sufficiently reproducible for further application in high-throughput molecular characterization of transgenic lines. Key words: HVA1, durum wheat, transgenic plant, real time polymerase chain reaction (PCR), drought.

Genetic differences between the wild and hatchery-produced populations of Korean short barbeled grunter (Hapalogenys nitens) determined with microsatellite markers.

Short barbeled grunter, Hapalogenys nitens, is an economically important fishery resource. In Korea, this fish is in the early stage of domestication, and it has been regarded as the candidate marine fish species for prospective aquaculture diversification. This study presents a preliminary investigation of the future viability of sustainable fry production from short barbeled grunter. We used 12 polymorphic nuclear microsatellite DNA loci to analyze the possible genetic variability between the wild and hatchery-produced populations of short barbeled grunter from Korea and identified 91 alleles. Compared to the wild population, significant genetic changes including reduced genetic diversity (average allele number: 7.42 vs 3.75; average expected heterozygosity: 0.713 vs 0.598, Wilcoxon signed-rank test; P < 0.05) and differentiation [overall fixation index (FST) = 0.088, P < 0.01] occurred in the hatchery-produced population, as indicated by the observation of allele richness, unique allele, heterozygosity, FST, and results of molecular analysis of variance. These findings indicate that genetic drift may have promoted the differentiation between these 2 populations, which may have negative effects on sustainable fry production. Therefore, genetic variations of the wild and hatchery-produced populations should be monitored and subjected to control inbreeding through a commercial breeding program. The information presented by this paper would provide a useful genetic basis for future sustainable culturing planning and management of H. nitens.

Phenotypic characterization of a mini cor collection for increased grain quality in maize

Agronomic traits of 18 populations comprising a mini core collection for increased grain quality of the Maize Research Institute Zemun Polje were studied, along with two standard kernel type commercial hybrids. For almost all the traits (except root lodging) a considerable genetic variability was found, enabling successful breeding for any of them using this populations. Based on the obtained results, two populations were found to have grain yield at the level of ZP 341 commercial hybrid (one of them is from former Yugoslavia, and another is the introduced one). These two populations will be first to introduce into commercial breeding programs, if it proves they have also favorable biochemical characteristics. On the other hand, three populations had grain yield in the range of 1, 60-1, 91 t/ha, that is even lower than for commercial inbreeds. They will be excluded from the further breeding programs. Most of the populations were earlier than the commercial hybrids, during vegetation and according to the grain moisture at harvest. This is very favorable from a breeding standpoint. The worst characteristic of the population was very high stalk lodging, compared to commercial checks.

The influence of genetic background versus commercial breeding programs on chicken immunocompetence

Immunocompetence of livestock plays an important role in farm profitability because it directly affects health maintenance. Genetics significantly influences the immune system, and the genotypic structure of modern fast-growing chickens has been changed, particularly after decades of breeding for higher production. Therefore, this study was designed to help determine if intensive breeding programs have adversely affected immunocompetence or whether the immune response profiles are controlled to greater extent by genetic background. Thus, 3 indigenous chicken populations from different genetic backgrounds and 2 globally available modern broiler strains, Ross 308 and Cobb 500, were evaluated for various aspects of immune response. These included antibody responses against sheep red blood cells and Brucella abortus antigen, as well as some aspects of cell-mediated immunocompetence by toe web swelling test and in vitro blood mononuclear cell proliferation. Significant differences (P < 0.05) in antibody responses to both antigens and cellular proliferation were observed among populations but not consistently between modern commercial strains versus the indigenous populations. In fact, the immune response profiles of Cobb 500 were similar to the indigenous populations, but varied compared with the other commercial strain. In addition, considerable variation was recorded between indigenous populations for all responses measured in this study. The results of this study suggest that the variation observed in immune responses between these strains of chickens is most likely due to differences in the genetic background between each strain of chicken rather than by commercial selection programs for high production.

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

Development of models to predict genotype by environment interactions, in unobserved environments, using environmental covariates, a crop model and genomic selection. Application to a large winter wheat dataset. Genotype by environment interaction (G*E) is one of the key issues when analyzing phenotypes. The use of environment data to model G*E has long been a subject of interest but is limited by the same problems as those addressed by genomic selection methods: a large number of correlated predictors each explaining a small amount of the total variance. In addition, non-linear responses of genotypes to stresses are expected to further complicate the analysis. Using a crop model to derive stress covariates from daily weather data for predicted crop development stages, we propose an extension of the factorial regression model to genomic selection. This model is further extended to the marker level, enabling the modeling of quantitative trait loci (QTL) by environment interaction (Q*E), on a genome-wide scale. A newly developed ensemble method, soft rule fit, was used to improve this model and capture non-linear responses of QTL to stresses. The method is tested using a large winter wheat dataset, representative of the type of data available in a large-scale commercial breeding program. Accuracy in predicting genotype performance in unobserved environments for which weather data were available increased by 11.1% on average and the variability in prediction accuracy decreased by 10.8%. By leveraging agronomic knowledge and the large historical datasets generated by breeding programs, this new model provides insight into the genetic architecture of genotype by environment interactions and could predict genotype performance based on past and future weather scenarios.