Commercial Breeding Programs Research Articles

301 Leveraging genomics to advance the breeding of Canadian livestock

Abstract Implementing breeding strategies for a more sustainable food system is one of the most pressing topics for livestock industries. Although different species face different challenges, large-scale research projects can pave the way for future opportunities in these key sectors. Herein, we present two examples (dairy and poultry) of how research projects can result in meaningful changes to commercial breeding programs. The first example is an international large-scale dairy project, which will deliver a roadmap for greenhouse gas (GHG) management using genomics and nutrition. The project aims to facilitate a 55% reduction in GHG emissions from Canadian dairy at an estimated value of $338M CAD. This systems-level approach will leverage resources developed through previous and current large-scale projects to produce accurate multi-level emission estimates and identify opportunities to mitigate enteric GHG emissions. The results of this project will provide accurate, reliable, and robust data for industry stakeholders, national policy, and GHG inventories. The second example is a research collaboration with a commercial turkey breeding company that will enable breeding strategies for long-term and sustainable genetic improvement in health traits. This project aims to reduce preslaughter mortality by 5% and condemnations due to myopathies and health issues. This reduction alone is expected to result in 7.5M kg more turkey meat at a value of $19.8M CAD. Furthermore, there is also an expected reduction of 2.3M kg of CO2 equivalent per year for each 1% livability improvement due to production efficiencies and reduced inputs wasted for more sustainable and ethical meat production. Overall, ongoing and future research initiatives will continue to deliver solutions for key Canadian livestock sectors to improve animal health and welfare as well as efficiency and sustainability. The strides made in these ongoing collaborative projects are imperative for enhancing the sustainability of animal agriculture to feed the growing population.

Effect of landraces on Musa micropropagation

This work aimed at assessing the performance of two landraces of Musa spp in micropropagation. Tissues from Owom and Efol were sterilized by soaking the explants in 70 % ethanol for 30 sec, 8 % NaOCl for 5 min, 5 g/L benlate for 5 min, and in 1.2 g/L HgCl2 for 10 min before being thoroughly washed with distilled water. Tissue exposure to U. V. light for 5 min was done before they were cultured in a shooting MS-based culture medium supplemented with 5.00 mg/L concentration of 6-Benzylaminopurine, and later to a rooting MS-based culture medium supplemented with indoleacetic acid (IAA) of 2.00 mg/l concentration. Data were collected on number of shoots, shoot height, shoot’s health, days to rooting, root number, and root length. The result from shooting medium showed that the plants’ heights were highly significantly different at P ≤ 0.01, with Owom producing marginal mean heights of 3.59 cm and 5.05 cm at 3 and 5 weeks respectively, after initiation. A very high significant difference was observed with plant health at P ≤ 0.001 whereby Owom landrace reduced in health status as the week increased, unlike Efol which increased in health status across the weeks. For rooting medium, significant differences at P ≤ 0.05 for days to rooting, root length, health performance, and plant height were observed. While high significant difference was observed for the number of roots at P ≤ 0.01. Owom performed significantly better than Efol and has shown value for commercial production and breeding programs.

Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopenaeus vannamei

Litopenaeus vannamei is one of the most economically productive species in aquaculture. It accounts for about 80% of the world's mariculture production of shrimp. Genetic selection of shrimp is mainly based on family selection. Therefore, accurate pedigree information is essential to ensure the reliability of estimated genetic parameters and the selection of the best broodstock. Recent advances in molecular breeding have facilitated molecular pedigree reconstruction based on SNPs and improved the accuracy of selection. However, breeding populations of aquatic species tend to be large. Therefore, a high-throughput and cost-effective method was needed for the commercial application of parentage assignment. In this study, we developed a low-density SNP panel based on target sequencing. A total of 200 amplicons, evenly distributed across the genome, were captured by multiplex PCR and sequenced by next-generation sequencing. Genotyping of 320 individuals in four ponds including multiple families identified 1,169 SNPs. Based on these SNPs, two softwares including Sequoia and PaternityT were used to reconstruct the sibling information. Consequently, a total of 39 families were accurately identified, and the results of the two software programs were highly consistent. Analysis based on different numbers of amplicons showed that at least 50 amplicons were required for accurate assignment. The identification result was also validated by principal component analysis and phylogenetic analysis. With the development of NGS technology, thousands of individuals could be genotyped with high throughput and low cost, making the method developed in this study affordable for parentage assignment in commercial breeding program. Meanwhile, the low-density SNP panel also has high value and prospects for application in shrimp genetic research.

New maize inbred development method I: Inter‐heterotic group composite and tester choice

AbstractCurrent maize (Zea mays L.) breeding methods and the limited germplasm infusion and mixing may slow the rate of genetic gain in the future. Using inter‐heterotic group composites for maize inbred development has been questioned because of the issue of choosing appropriate testers. However, three observations can be revisited to facilitate the exploration of alternative methods. First, since the adoption of single‐cross hybrids and the establishment of heterotic groups, the amount of heterosis has only been increasing slightly. Second, genomic analysis indicated the frequencies of the favorable alleles had significantly increased after a century's breeding. Third, the divergence of maize heterotic groups was preceded by the merging of landraces and diverse inbreds, after which three major heterotic groups were established. The objective of this study was to design different scenarios to generate inter‐heterotic group composites and evaluate their usefulness in the commercial breeding program. We investigated two methods: the inter‐heterotic group composite method (termed as super population [SupPop]) and the modified SupPop method (ModiSP, that is, backcrossing SupPop lines with elite inbreds). The results showed that the best scenario for the SupPop method was to use the SupPop inbreds to cross with a tester from the B14 group. When all four heterotic groups were mixed, the favored tester was from stiff stalk. However, ModiSP showed a higher chance of producing the best yield performance. These empirical results suggest that solutions can be proposed to identify the testers so that using inter‐heterotic group composites for inbred development can be considered.

Characterizing stay-green in barley across diverse environments: unveiling novel haplotypes

Key messageThere is variation in stay-green within barley breeding germplasm, influenced by multiple haplotypes and environmental conditions. The positive genetic correlation between stay-green and yield across multiple environments highlights the potential as a future breeding target.Barley is considered one of the most naturally resilient crops making it an excellent candidate to dissect the genetics of drought adaptive component traits. Stay-green, is thought to contribute to drought adaptation, in which the photosynthetic machinery is maintained for a longer period post-anthesis increasing the photosynthetic duration of the plant. In other cereal crops, including wheat, stay-green has been linked to increased yield under water-limited conditions. Utilizing a panel of diverse barley breeding lines from a commercial breeding program we aimed to characterize stay-green in four environments across two years. Spatiotemporal modeling was used to accurately model senescence patterns from flowering to maturity characterizing the variation for stay-green in barley for the first time. Environmental effects were identified, and multi-environment trait analysis was performed for stay-green characteristics during grain filling. A consistently positive genetic correlation was found between yield and stay-green. Twenty-two chromosomal regions with large effect haplotypes were identified across and within environment types, with ten being identified in multiple environments. In silico stacking of multiple desirable haplotypes showed an opportunity to improve the stay-green phenotype through targeted breeding. This study is the first of its kind to model barley stay-green in a large breeding panel and has detected novel, stable and environment specific haplotypes. This provides a platform for breeders to develop Australian barley with custom senescence profiles for improved drought adaptation.

Maximizing efficiency in sunflower breeding through historical data optimization

Genomic selection (GS) has become an increasingly popular tool in plant breeding programs, propelled by declining genotyping costs, an increase in computational power, and rediscovery of the best linear unbiased prediction methodology over the past two decades. This development has led to an accumulation of extensive historical datasets with genotypic and phenotypic information, triggering the question of how to best utilize these datasets. Here, we investigate whether all available data or a subset should be used to calibrate GS models for across-year predictions in a 7-year dataset of a commercial hybrid sunflower breeding program. We employed a multi-objective optimization approach to determine the ideal years to include in the training set (TRS). Next, for a given combination of TRS years, we further optimized the TRS size and its genetic composition. We developed the Min_GRM size optimization method which consistently found the optimal TRS size, reducing dimensionality by 20% with an approximately 1% loss in predictive ability. Additionally, the Tails_GEGVs algorithm displayed potential, outperforming the use of all data by using just 60% of it for grain yield, a high-complexity, low-heritability trait. Moreover, maximizing the genetic diversity of the TRS resulted in a consistent predictive ability across the entire range of genotypic values in the test set. Interestingly, the Tails_GEGVs algorithm, due to its ability to leverage heterogeneity, enhanced predictive performance for key hybrids with extreme genotypic values. Our study provides new insights into the optimal utilization of historical data in plant breeding programs, resulting in improved GS model predictive ability.

Integrated alternative approaches to select feed-efficient rainbow trout families to enhance the plant protein utilization

Improving feed utilization efficiency is a challenge in aquaculture. Therefore, we developed an indirect benchmark to use in selecting trout for improved efficiency of feed utilization on plant protein (soy)-based diets, with the long-term goal of reducing the cost of commercial trout production. We used a four-part integrative approach to identify feed efficient individuals among 1595 fish coming from 12 genetically selected families by establishing the phenotypic relationship between feed conversion ratio (FCR) and body weight variations using compensatory feeding regimes. Additionally, we examined the nutritional composition of fish filet for each efficiency phenotype during the compensatory regimen. Our findings showed that the fish with the lowest weight loss during a feed deprivation period and the highest weight gain during the refeeding period (FD−/RF +) demonstrated the lowest FCR (FCR = 0.99) and consisted of individuals from several lines. This finding confirms the possibility of improving feed efficiency in mixed lines. Although feeding period has an effect on nutritional composition of fillet, such selection criteria did not show an effect on groups. Overall, successful selection for the improvement of feed efficiency will have a broad application to commercial fish selective breeding programs, leading to increased aquaculture sustainability in the long run.

Large-Scale Evaluation of Indonesian Elite Maize Breeding Lines for Resistance Against Bacterial Stalk Rot Caused by Dickeya zeae

Bacterial stalk rot is one of the important diseases in maize caused by <em>Dickeya zeae</em>. Infection of this disease can lead to a considerable amount of loss in yield, with up to 98 percent loss of yield. The use of resistant materials is the most effective approach to managing bacterial stalk rot in maize. This study evaluates a large-scale phenotypic screening of 624 maize lines against bacterial stalk rot, divided into two groups based on a heterotic pool. These lines are used in a commercial breeding program in Indonesia. This study develops a stabbing method with a large gauge hypodermic needle, allowing for scalability in delivering inoculum while performing large-scale line evaluation. The result from ANOVA reveals a significant (P<0.05) effect of lines, day after infection, and interaction between day after infection and group. Group two displays fewer resistant lines compared to group one. This work presents a method for large-scale line evaluation for resistance against bacterial stalk rot, where the information obtained can be used in industrial breeding programs for routine material screening during the development of new lines or hybrids and for genomic studies of bacterial stalk rot resistance.

Genetic improvement of duration of fertility in chickens and its commercial application for extending insemination intervals

The growth rate of chickens has made remarkable progress in recent decades through continuous breeding efforts. However, this advancement has also led to a decline in fertility among commercially bred chickens. Therefore, it is crucial to understand and improve factors that influence fertility to ensure the continued success of the industry. Here, we conduct a 3-generation selection experiment within 2 purebred female lines, with the aim of increasing the duration of fertility (DF). Duration of fertility refers to the length of time hens remain capable of producing fertilized eggs and is a crucial factor that directly impacts chick output. The results showed that significant genetic progress was achieved in embryo survival rates and the fertility duration day during both the peak and late laying periods. Moreover, after 3 generations of selective breeding, the disparities in embryo survival and chick health rates from setting eggs between 8-d and 5-d insemination intervals in the grandparent stock were significantly reduced. The rates decreased from 1.83% and 2.39 to 0.72% and 0.33%, respectively. Surprisingly, the hatching performances of hens with an 8-d interval were comparable to those hens that had not undergone genetic selection for DF and had a 5-d interval. We further discussed the possibility of extending the insemination interval to 8 d in parent stock for commercial practices. The parental populations exhibited remarkable performance in terms of percentages of embryo survival and healthy chicks from the setting eggs, with rates exceeding 94 and 90%, respectively. Thus, it can be inferred that an extended insemination interval is feasible by genetic selection for DF. These findings will provide valuable insights into the efficacy of genetic selection in enhancing DF and its practical application in commercial breeding programs.

Selection of heat tolerant donor lines in indian mustard (Brassica Juncea L.)

Heat stress during the post anthesis (seed filling) stage negatively influences the movement of photosynthates to the developing sinks and, thus lowering the seed yield in Indian mustard [Brassica juncea (L.) Czern & Coss]. The present studywas conducted with the objective to unravel the variability for terminal heat stress (THS) in a fixed diversitygenetic stock of 500 lines of Indian mustard. Germplasm stock exhibited huge variability for seed yield and its contributing traits with variable levels of yield reduction under late sown conditions. The per se yield based computed heat stress susceptibility index (HSI) ranged from 32.3 (highly THS susceptible) to -1.15 (THS tolerant). Based on yield reduction due to THS, 500 test genotypes were grouped into 10 classes and genotypes from each class wererandomly takento constitute a diverse panel of 96 lines. This panel was evaluated under THS by raising crop underpoly-tunnels during reproductive phase along with same set of 96 genotypes raised under normal field conditions (served as control). Based on agronomic advantage and HSI for economic traits, 23 heat tolerant donor lines were selected for utilization in commercial breeding programme. Bangladesh J. Bot. 52(4): 1007-1013, 2023 (December)

Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet.

Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses. Here, GCA was estimated as the sum of additive genetic effects and within-group epistasis due to high degree of inbreeding in parental lines. SCA was estimated as the sum of across-group epistasis and dominance effects. Three models were compared. In model 1, it was assumed that each hybrid was produced from two completely inbred parental lines. Model 1 was extended to include three-way hybrids from parental lines with arbitrary levels of inbreeding: In model 2, parents of the three-way hybrids could have any levels of inbreeding, while the grandparents of the maternal parent were assumed completely inbred. In model 3, all parental components could have any levels of inbreeding. Data from commercial breeding programs for hybrid rye and sugar beet was used to evaluate the models. The traits grain yield and root yield were analyzed for rye and sugar beet, respectively. Additive genetic variances were larger than epistatic and dominance variances. The models' predictive abilities for total genetic value, for GCA of each parental line and for SCA were evaluated based on different cross-validation strategies. Predictive abilities were highest for total genetic values and lowest for SCA. Predictive abilities for SCA and for GCA of maternal lines were higher for model 2 and model 3 than for model 1. The implementation of the genomic prediction models in hybrid breeding programs can potentially lead to increased genetic gain in two different ways: I) by facilitating the selection of crossing parents with high GCA within heterotic groups and II) by prediction of SCA of all realized and potential combinations of parental lines to produce hybrids with high total genetic values.

Mapping of the gene in tomato conferring resistance to root-knot nematodes at high soil temperature.

Root-knot nematodes (RKNs, Meloidogyne spp.) can cause severe yield losses in tomatoes. The Mi-1.2 gene in tomato confers resistance to the Meloidogyne species M. incognita, M. arenaria and M. javanica, which are prevalent in tomato growing areas. However, this resistance breaks down at high soil temperatures (>28°C). Therefore, it is imperative that new resistance sources are identified and incorporated into commercial breeding programmes. We identified a tomato line, MT12, that does not have Mi-1.2 but provides resistance to M. incognita at 32°C soil temperature. An F2 mapping population was generated by crossing the resistant line with a susceptible line, MT17; the segregation ratio showed that the resistance is conferred by a single dominant gene, designated RRKN1 (Resistance to Root-Knot Nematode 1). The RRKN1 gene was mapped using 111 Kompetitive Allele Specific PCR (KASP) markers and characterized. Linkage analysis showed that RRKN1 is located on chromosome 6 and flanking markers placed the locus within a 270 kb interval. These newly developed markers can help pyramiding R-genes and generating new tomato varieties resistant to RKNs at high soil temperatures.

Exploring GWAS and genomic prediction to improve Septoria tritici blotch resistance in wheat

Septoria tritici blotch (STB) is a destructive foliar diseases threatening wheat grain yield. Wheat breeding for STB disease resistance has been identified as the most sustainable and environment-friendly approach. In this work, a panel of 316 winter wheat breeding lines from a commercial breeding program were evaluated for STB resistance at the seedling stage under controlled conditions followed by genome-wide association study (GWAS) and genomic prediction (GP). The study revealed a significant genotypic variation for STB seedling resistance, while disease severity scores exhibited a normal frequency distribution. Moreover, we calculated a broad-sense heritability of 0.62 for the trait. Nine single- and multi-locus GWAS models identified 24 marker-trait associations grouped into 20 quantitative trait loci (QTLs) for STB seedling-stage resistance. The seven QTLs located on chromosomes 1B, 2A, 2B, 5B (two), 7A, and 7D are reported for the first time and could potentially be novel. The GP cross-validation analysis in the RR-BLUP model estimated the genomic-estimated breeding values (GEBVs) of STB resistance with a prediction accuracy of 0.49. Meanwhile, the GWAS assisted wRR-BLUP model improved the accuracy to 0.58. The identified QTLs can be used for marker-assisted backcrossing against STB in winter wheat. Moreover, the higher prediction accuracy recorded from the GWAS-assisted GP analysis implies its power to successfully select superior candidate lines based on their GEBVs for STB resistance.

Yield performance and agronomic characteristics of several candidate hybrid maize varieties on uncultivated land

Corn is currently a strategic and dominant national commodity used as raw material for animal feed. The increase in productivity was made possible by the continued assembly of hybrid corn which has a higher production per hectare with a wide or site-specific adaptation rate. Due to the wide utilization of maize, the main objective of all commercial maize breeding programs is to obtain new inbred and hybrids which will outperform the hybrids mainly on grain yield characteristics. This research was conducted in Bone Regency to know the yield potential of several hybrid maize on uncultivated land, using a randomized block design, 4 replications, a plot area of 3 x 5 m, and spacing of 70 x 20 cm. The material used consisted of 4 hybrids and 2 comparison varieties. The results showed that the hybrid G1603 (11.61 t/ha) showed the highest grain yield and was not significantly different from the comparison varieties. This result was supported by the character of the number of rows of seeds per ear, the length of the ear, and the diameter. These characteristics need to be considered to get hybrid corn with a high grain yield.

Isogenic lines of rainbow trout (Oncorhynchus mykiss) as a tool to assess how growth and feeding behaviour are correlated to feed efficiency in fish

Accurately measuring individual feed intake is required to include feed efficiency (FE) as an objective in commercial breeding programs. Phenotyping individual feed intake through direct measurements remains complex in fish reared in groups. One way to overcome this challenge is to find proxies for estimating FE. This study aimed to investigate the correlations between fish FE and potential predictive criteria in rainbow trout Oncorhynchus mykiss. As predictive criteria, we considered the variations of body weight assessed as thermal growth coefficients (TGC) and the feeding behaviour assessed as the number of feed demands over a period and the proportion of the demands made before noon. Feed intake was assessed over three different periods in ten isogenic lines allowing a recording for each of the ten genotypes while keeping fish in groups. The protocol consisted of two successive feed deprivation and refeeding phases after initial basal growth periods. Correlations were then calculated between FE, measured either as feed conversion ratio (FCR) or residual feed intake (RFI), and the different indirect criteria. We found positive phenotypic correlations between FCR and RFI over the feed intake measurement periods (r ⩾ 0.79, P < 0.001). Assessment of the relationship between FE traits (FCR and RFI) calculated over the three measurement periods and TGC revealed no significant association. Regarding feeding behaviour, significant differences in the daily profile of feed demands and their numbers were found among the ten isogenic lines. RFI calculated from the first feed intake measurement period and feeding behaviour, assessed as the number of feed demands were positively correlated (r = 0.42–0.49, P ⩽ 0.022). Nevertheless, such correlations were not established for the two other measurement periods following feed deprivation. While we demonstrated that the weight variations during feed deprivation are not a good proxy for FE (FCR or RFI) in rainbow trout, we also highlighted the interest in exploring more the relationships between FE and feeding behaviour in fish.

HCG versus histrelin acetate: ovulation inducing agents in mares (Equus caballus) in a commercial breeding program in Uruguay

Hormonal control of ovulation timing is an effective tool to optimize reproductive management and reduce costs in equine breeding programs. Few studies have evaluated the efficacy of GnRH analog histrelin as an ovulation inducer agent. This study aimed to compare the efficacy of human chorionic gonadotrophin (hCG) and histrelin as ovulation inducers in young, adult, and old mares during spring and summer. Reproductive records of 321 estrous cycles of 125 mares, mean age 9.8±0.37 years, range 1.5–24 years, between 360-600 kg body weight, and body condition ≥3 (1/5), were evaluated during spring (151 cycles) and summer (170 cycles). Mares were kept in the field and fed alfalfa hay, balanced concentrate feed and ad-libitum water. The ovaries, uterus, and cervix underwent transrectal examination and ultrasonography daily. When only one dominant follicle of 35 mm and endometrial edema compatible with estrus were reached, ovulation was induced. Each cycle was monitored every two to six hours until ovulation, 24h after induction. Cycles were randomly allotted in two groups; G1 (n=106 cycles): 1500 IU hCG (IV); G2 (n=215 cycles): 250 μg histrelin acetate (IM). A total of 119 cycles were from young (<8 years), 93 from adults (8-15 years), and 109 from old mares (>15 years). Cycles of mares ovulating within 24-48hafter treatment were considered to have responded to the inducer, and those ovulating before 24h and after 48h were excluded from the experiment. Inducer agents, season (spring or summer), and mare age were independent factors, and ovulation between 24-48h was considered the dependent factor. Data were analyzed through Fisher's exact test. The significance level was defined as P<0.05. From the 321 induced cycles, 254 (79.1%) ovulated within 24-48h, 20 (6.2%) before 24h, and 47 (14.6%) after 48h. There were no differences (P=0.2414) in the average response time between G1 (37.2h±3,5) and G2 (39.3h±4,5). The ovulatory response between G1 and G2 did not differ in spring (84.1% versus 90.7%, P=0.2627) and summer (79.2% versus 85.4%, P=0.3534). Independent of the inducer, the season did not influence the ovulation response in the different mare ages (spring P=0.1489; summer P=0.2992). No differences (P=0.896) were found between drugs in young and adult mares. However, old mares had a higher percentage of ovulatory response in spring and summer to histrelin (n=76) than to hCG (n=24) (89.5% versus 45.8%, P<0.0001). In conclusion, histrelin is more effective and accurate in inducing ovulation in old mares (>15 years) than hCG throughout the breeding season.

Efficacy of buserelin for induction of ovulation in mares

The rational and controlled management of equine reproduction in commercial programs promotes the development of drugs that help to regulate certain physiological processes in mares, such as luteolysis or ovulation. Human Chorionic Gonadotropin is used predominantly in commercial and experimental programs showing optimal ovulatory results in multiple studies. However, a lower inducing effect has been reported in old mares, which are highly represented in the commercial breeding population. Some studies with human formulations of buserelin, one of the oldest GnRH synthetic analogs, have demonstrated similar efficacy to other analogs in mares (Newcombe and Cuervo-Arango. Journal of Equine Veterinary Science. 2016; 41, 57). In Argentina, until now, there are no specific buserelin formulations for mares. The aim of this clinical prospective study was to compare the ovulation induction efficacy of two doses of a new buserelin formulation in mares of different age groups. The study was carried out in a commercial breeding program in the subtropical north of Argentina using healthy Quarter Horse and Criollo mixed breed mares randomly assigned to treatment groups. When uterine edema, a relaxed cervix and 35 mm follicles were detected, mares were induced once, with a single intravenous (IV) injection of 0.2mg of buserelin (Busereleq,Laboratorio CIMOL, Argentina) for group 1 (G1, n=77) and 0.4mg for group 2 (G2, n=54). The response was considered positive when absence of the dominant follicle and presence in the same ovary of a corpus luteum were detected by ultrasound, 48 hours after treatment. In both groups, mares were classified according to age in <10; 11-15; >15 years old (yo). The data were analyzed by the chi square test for categorized data using Infostat Software. The follicular size, degree of edema and age were compared in the different groups at the time of treatment by means of a non-parametric Kruskal-Wallis analysis of variance. The results showed that 87.01% of the G1 (0,2 mg) and 70.37% of G2 (0.4mg) mares responded positively (p<0.05). No significant differences were found between follicular size, degree of edema and age of the mares at the time of induction among treated groups (p >0.05). Efficacy of the different treatments by age group in G1 and G2 was 77% and 68% in <10 y.o; 96% and 71% in 10 -15 y.o; 90% and 73% in >15 y.o respectively. A significant difference among treated groups was detected in middle age (10-15 years) with more efficacy in G1 (p=0,017). Our results suggest that a low dose buserelin (0.2mg IV) can be used to induce ovulation with acceptable clinical efficacy, even in older mares.

Successful use of sexed stallion semen for in vitro embryo production; a preliminary study

The use of sex-sorted semen to obtain offspring of a desired sex in commercial livestock breeding programs has been in a state of rapid growth as sorting technology has evolved (Neculai-Valeanu and Ariton, Animals 2021, 11, 1182-1194, 2021). In horses, sex-sorted semen has resulted in successful pregnancies using low-dose or hysteroscopic artificial insemination, albeit with decreased pregnancy rates (Clulow et al, Animal Reproduction Science 108: 287–297, 2008; Gibb et al, Eq Vet J 49:160–166, 2017). Even though sex-sorted semen has been used to produce viable in vitro produced (IVP) embryos, the cleavage and blastocyst rates remain low (Colleoni et al, Reproduction, Fertility and Development 21(1): 228-229, 2008). Using current sperm sorting technology (ST Inc, Navasota, TX), we investigated fertilization, cleavage, and embryo development rates after ICSI using a time-lapse imaging system. To sex sort the semen, the ejaculate was diluted in 1:1 in a casein/cholesterol-based semen extender (BotuSemen Gold) supplemented with 60ug/ml of Hoechst 33342. The diluted semen was centrifuged through a colloid suspension (EquiPure) for 25 min at 300g using 3mL of EquiPure per billion sperm. After centrifugation, the sperm pellet was split into two aliquots: NON-SEXED, resuspended in BotuCrio, cooled and frozen in 0.5 ml straws at ∼ 100 million/ml, and SEXED, resuspended in a proprietarychemically-defined medium (EquiShip, ST Genetics), and transported to the sorting facility at ∼20°C. At the laboratory, the sperm were passed through the SexedULTRA™ Genesis III flow cytometer. After approximately 40 million total events X- and Y-bearing sperm were recovered, diluted in BotuCrio at a concentration of 2 million/ml, loaded into 0.5 ml straws and frozen. Oocytes were obtained from mares using transvaginal ultrasound-guided aspiration, shipped/held for 24h, followed by in vitro maturation. The matured MII oocytes from each aspiration were randomly split and injected with SEXED and NONSEXED sperm. A total of 56 oocytes were fertilized. We observed 24/29 and 23/27 cleaved oocytes, resulting in 11 and 12 blastocysts in SEXED and NONSEXED groups, respectively. No significant difference was detected in the cleavage and blastocyst rates among the groups. Embryo kinetic analysis revealed a slightly shorter duration from injection to blastocyst formation in the SEXED versus NONSEXED groups (183h and 188h, respectively). Higher number of embryos are required to compare the morpho-kinetics of male and female embryos at each developmental stage. This is a preliminary report, showing the successful use of frozen sexed semen in a commercial in vitro embryo production setting and further studies are ongoing.

Genomic prediction for drought tolerance using multienvironment data in a common bean (Phaseolus vulgaris) breeding program

AbstractThis work evaluated the efficiency of different genomic prediction (GP) methods in a diverse Mesoamerican panel of 339 common bean accessions, genotyped with 3398 SNP markers. Field experiments were carried out for three consecutive years, with adequate water supply (non‐stress—NS) and water restriction imposition (water‐stress—WS), analyzing seed weight (SW) and grain yield (GY). Two methods to predict the accuracies (rĝg) were adopted (GBLUP and Bayes) and also considered the environmental variation (GBLUP‐based reaction norm model). Similar accuracies were observed for both methods. For GY, the highest rĝg were detected under NS (rĝg = 0.49) in 2016 (rĝg = 0.49) and in the joint analysis for the WS condition (rĝg = 0.33), both for models using local landraces. For SW under NS, the rĝg was higher for the elite lines (rĝg = 0.72), whereas for WS, the rĝg dropped considerably, ranging from 0.45 to 0.61 for the joint analysis, considering the landraces and all samples, respectively. For GY and SW, under NS, the rĝg using both models increased with increasing number of SNPs, until reaching a plateau of 800 and 300 SNPs, respectively. Increasing the training population (TP) size resulted in greater accuracy. Taking in account the Genotype × Environment, the multienvironment model performed better especially for more complex traits (GY/NS: rĝg = 0.32). The GP approach has great potential to help commercial bean breeding programs improving the performance of target quantitative traits.

Maintenance of UK bread baking quality: Trends in wheat quality traits over 50 years of breeding and potential for future application of genomic-assisted selection.

Improved selection of wheat varieties with high end-use quality contributes to sustainable food systems by ensuring productive crops are suitable for human consumption end-uses. Here, we investigated the genetic control and genomic prediction of milling and baking quality traits in a panel of 379 historic and elite, high-quality UK bread wheat (Triticum eastivum L.) varieties and breeding lines. Analysis of the panel showed that genetic diversity has not declined over recent decades of selective breeding while phenotypic analysis found a clear trend of increased loaf baking quality of modern milling wheats despite declining grain protein content. Genome-wide association analysis identified 24 quantitative trait loci (QTL) across all quality traits, many of which had pleiotropic effects. Changes in the frequency of positive alleles of QTL over recent decades reflected trends in trait variation and reveal where progress has historically been made for improved baking quality traits. It also demonstrates opportunities for marker-assisted selection for traits such as Hagberg falling number and specific weight that do not appear to have been improved by recent decades of phenotypic selection. We demonstrate that applying genomic prediction in a commercial wheat breeding program for expensive late-stage loaf baking quality traits outperforms phenotypic selection based on early-stage predictive quality traits. Finally, trait-assisted genomic prediction combining both phenotypic and genomic selection enabled slightly higher prediction accuracy, but genomic prediction alone was the most cost-effective selection strategy considering genotyping and phenotyping costs per sample.