Sustainable Breeding Research Articles

Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

Genetic admixture and performance diversity of high yielding dairy cows surrounding the Baghabari Milk Vita areas of Bangladesh

This study was planned to clarify the recent milk and reproductive performances of high yielding dairy crossbreds based on various genotype, parity and location beside the Baghabari Milk Vita areas of Bangladesh. Performance records were collected from total 81 crossbred cows from both 15 households in Sirajgonj and Pabna districts, and six bathan areas at Sirajgonj. Genetic admixture of various breeds identified in the studied areas showed diverse performance. Milk production not varied statistically (16.27 to 19.33 liters per day as peak) either for genotype, parity or region but differed in number of AI services for last pregnancy in L×HF×SL (1) and L×HF×JE (2.18) genotypes at household level. Average 70 days observed between the day of calving and next fertile AI service in dairy farming. The study on bathan revealed about 23 months for age at first fertile AI in high yielding dairy cows with average 1.92 AI services per cow for last conceive. Peak milk production identified in HF crossed with local than HF×SL and JE genotypes. Screening, record keeping and controlled AI or mating with specific targeted breed could increase breed uniformity and productivity of high yielding crossbreds not only in Milk Vita region but also other milk pocket areas of this country. In addition, breed composition study is required for ensuring specific breed effects on production performance to design a planned breeding for sustainable dairy breed development in Bangladesh.Asian J. Med. Biol. Res. March 2017, 3(1): 127-133

Development of a sequence-tagged site (STS) marker for sex identification in the dioecious rattan species Calamus guruba Buch.-Ham.

Calamus guruba Buch.-Ham., a perennial, dioecious rattan species of the family Arecaceae has recently emerged as an important source of tribal economy owing to its high-quality flexible canes for furniture manufacturing and cottage industries. The dioecious nature together with disproportionate distribution of male and female sex organs has been the major constraint in the development of an effective breeding programme for the plant. Early identification of the male and female genotypes at the seedling stage is a pre-requisite to ensure genetic improvement of C. guruba. In the present study, we used 30 inter simple sequence repeat (ISSR) markers to develop a sequence-tagged site (STS) linked to male sex in C. guruba. Molecular analysis of bulked DNA pooled from male and female genotypes resulted in the isolation of a putative male-specific marker CgMSM. Partial sequencing of CgMSM resulted in an STS marker CgMY1 which could successfully amplify a 597-bp fragment in male but not in the female plants. DNA gel blot analysis confirmed it as a single-copy locus in the male genome of C. guruba. Further validation of CgMY1 in the natural population of C. guruba resulted in precise detection of 9 males and 6 females from 15 individuals with unknown sex. Therefore, the STS marker CgMY1 could be used as a proficient tool for early sex differentiation and form the basis of a sustainable breeding programme for genetic improvement of C. guruba.

Quantitative conservation genetics of wild and managed bees

Quantitative genetic traits provide insights into the evolutionary potential of populations, as heritability estimates measure the population’s ability to respond to global changes. Although wild and managed bees are increasingly threatened by the degradation of natural habitats and climate change, risking plant biodiversity and agriculture production, no study has yet performed a systematic review of heritability estimates across the group. Here we help fill this knowledge gap, gathering all available heritability estimates for ants, bees, and wasps, evaluating which factors affect these estimates and assessing the reported genetic correlations between traits. Using a model selection approach to analyze a dataset of more than 800 heritability estimates, we found that heritability is influenced by trait type, with morphological traits exhibiting the highest heritability estimates, and defense and metabolism-related traits showing the lowest estimates. Study system, sociality degree, experimental design, estimation type (narrow or broad-sense heritability), and sample size were not found to affect heritability estimates. Results remained unaltered when correcting for phylogenetic inertia, and when analyzing social bees separately. Genetic correlations between honeybee traits revealed both positive coefficients, usually for traits in the same category, and negative coefficients, suggesting trade-offs among other traits. We discuss these findings and highlight the importance of maintaining genetic variance in fitness-related traits. Our study shows the importance of considering heritability estimates and genetic correlations when designing breeding and conservation programs. We hope this meta-analysis helps identify sustainable breeding approaches and conservation strategies that help safeguard the evolutionary potential of wild and managed bees.

Sustainable breeding objectives and possible selection response: Finding the balance between economics and breeders' preferences.

To optimize breeding objectives of Fleckvieh and Brown Swiss cattle, economic values were re-estimated using updated prices, costs, and population parameters. Subsequently, the expected selection responses for the total merit index (TMI) were calculated using previous and newly derived economic values. The responses were compared for alternative scenarios that consider breeders' preferences. A dairy herd with milk production, bull fattening, and rearing of replacement stock was modeled. The economic value of a trait was derived by calculating the difference in herd profit before and after genetic improvement. Economic values for each trait were derived while keeping all other traits constant. The traits considered were dairy, beef, and fitness traits, the latter including direct health traits. The calculation of the TMI and the expected selection responses was done using selection index methodology with estimated breeding values instead of phenotypic deviations. For the scenario representing the situation up to 2016, all traits included in the TMI were considered with their respective economic values before the update. Selection response was also calculated for newly derived economic values and some alternative scenarios, including the new trait vitality index (subindex comprising stillbirth and rearing losses). For Fleckvieh, the relative economic value for the trait groups milk, beef, and fitness were 38, 16, and 46%, respectively, up to 2016, and 39, 13, and 48%, respectively, for the newly derived economic values. Approximately the same selection response may be expected for the milk trait group, whereas the new weightings resulted in a substantially decreased response in beef traits. Within the fitness block, all traits, with the exception of fertility, showed a positive selection response. For Brown Swiss, the relative economic values for the main trait groups milk, beef, and fitness were 48, 5, and 47% before 2016, respectively, whereas for the newly derived scenario they were 40, 14, and 39%. For both Brown Swiss and Fleckvieh, the fertility complex was expected to further deteriorate, whereas all other expected selection responses for fitness traits were positive. Several additional and alternative scenarios were calculated as a basis for discussion with breeders. A decision was made to implement TMI with relative economic values for milk, beef, and fitness with 38, 18, and 44% for Fleckvieh and 50, 5, and 45% for Brown Swiss, respectively. In both breeds, no positive expected selection response was predicted for fertility, although this trait complex received a markedly higher weight than that derived economically. An even higher weight for fertility could not be agreed on due to the effect on selection response of other traits. Hence, breeders decided to direct more attention toward the preselection of bulls with regard to fertility.

Genetic parameters for large white pigs reared under intensive management systems in Kenya

ABSTRACTA lack of performance parameters is one of the factors limiting the implementation of sustainable breeding strategies for the pig industry in Kenya. The objective of this study was to estimate genetic and phenotypic parameters for growth performance of Large White pigs reared under intensive management systems in Kenya. Growth performance data of 1398 pigs with 10 428 records were obtained from the Kenya Agricultural and Livestock Research Organization (KALRO)-Naivasha. Random regression models were used to estimate variance components by fitting different orders of Legendre polynomials. Phenotypic variance increased with age from 3.43±0.28 to 2449.28±392.07, while direct heritability ranged between 0.20±0.04 and 0.52±0.08. Maternal heritability increased from 0.26±0.05 to 0.79±0.04 while permanent environmental heritability was between 0±0.01 and 0.15±0.10. Genetic correlations were greater than 0.48 between all weights and decreased with an increase in age intervals. The first three eigenvalues ...

Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

We report here the genetic characterization of bitter gourd (Momordica charantia) based on polymorphisms of 50 simple sequence repeat (SSR) loci in 114 accessions that included landraces, breeding lines, and commercial open-pollinated and F1 hybrid cultivars widely grown in Asia. Neighbor-joining tree analysis revealed a high level of genetic variability in the collection. The 114 accessions formed three subpopulations represented by five clusters. Distribution of accessions across the five clusters reflected their geographic origin to a large extent. South Asian accessions originating from India, Bangladesh, and Pakistan were more closely related to each other than to any other geographical group. Likewise, southeast Asian accessions that originated from Cambodia, Vietnam, Indonesia, and Philippines were grouped together. Accessions that originated from Taiwan were genetically distinct and grouped separately. A landrace from Laos was genetically close to the accessions from Thailand and genetically distinct from the rest of the accessions. White-fruited genotypes were genetically distinct from green- and dark green–fruited genotypes. Low- and medium-bitter accessions were more similar to each other than to the high-bitter genotypes. Accessions with cylindrical fruit were genetically distinct from those with spindle or elongated fruit. Commercial cultivars in each cluster were closely related, which indicated a narrowing of the bitter gourd genetic base in Asia in response to market demands for uniformity and yield. Use of diverse germplasm resources in bitter gourd breeding will help in sustainable breeding and production.

P4034 Milk protein polymorphisms in African indigenous cattle: Opportunity for Sustainable Breeding Program

P4034 Milk protein polymorphisms in African indigenous cattle: Opportunity for Sustainable Breeding Program

P4041 Pooled whole-genome sequencing reveals molecular signatures of natural adaptive selection in Djallonke sheep of Ghana

The Djallonke sheep is of high socioeconomic and cultural importance in at least 14 countries within the sub-Saharan region of Africa, mainly because it is well adapted to the harsh environmental conditions and major livestock disease within this region. The larger-framed Sahelian sheep breed that cohabits large parts of the region is less adapted to all these challenges. The most prominent among these adaptive attributes is resistance to trypanosomiasis and helminthosis, two parasitic diseases, which collectively cost the worldwide animal production industry billions of dollars annually. Here we sequenced and pooled whole genomic DNA from five individuals each of Djallonke and Sahelian sheep breeds sampled from Ghana, at greater than 22-fold average coverage on an ion proton sequencer. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian, respectively, were successfully mapped to the sheep reference genome OviAri3. Preliminary analysis of the sequenced data of Djallonke breed showed several potential selective sweeps, some of which are co-localized within genomic regions known to harbor genes that mediate immune response in sheep. To the best of our knowledge, this is the first-ever whole-genome sequencing of these two sheep breeds. Our ongoing analysis of the sequenced data will provide a valuable resource for elucidating the underlying mutations and mechanisms of the numerous adaptive traits of the Djallonke sheep. This knowledge will not only ensure the sustainable breeding and utilization of the Djallonke sheep but will also have a long-term implication for the food security and poverty alleviation of all the 14 countries in the sub-Saharan African region.

Genetic testing in veterinary dermatology.

Molecular genetics has made significant advances in the analysis of hereditary dermatoses during the last several years. To provide an update on currently available genetic tests for skin diseases of dogs, cats and horses, and to aid the veterinary clinician in the appropriate selection and applications of genetic tests. The scientific literature on the topic was critically reviewed. The list of known causative variants for genodermatoses and hair morphology traits was compiled by searching the Online Mendelian Inheritance in Animals (OMIA) database. Genetic testing has become an important diagnostic method in veterinary medicine. Genetic tests can help to establish the correct diagnosis in some diseases with relatively nonspecific signs. Genetic tests are also essential for sustainable breeding programmes and to help minimize the frequency of animals with hereditary diseases. Advances in genetic methodology and bioinformatics already allow genome-wide screening for potential disease causing mutations for research purposes. It is anticipated that this will become a routine process in clinical practice in the future. As specific DNA tests and broad genome-wide analyses come into more common use, it is critical that clinicians understand the proper application and interpretation of these test results.

A categorisation and evaluation of rhino management policies

ABSTRACTRhino populations are at a critical level and new approaches are needed to ensure their survival. This study conducts a review and categorisation of policies for the management of rhinos. Twenty-seven policies are identified and classified into in-situ (reserve-based) and ex-situ (market-based) policies. The policies are then evaluated based on four target areas: poachers/hunters, consumers, intermediaries and the game reserves themselves. The study finds that protected area management policies seem most beneficial in the short run, in particular the enforcement of private property rights over resource utilisation, as well as the establishment of wildlife sanctuaries that act as sustainable breeding grounds for rhino populations.

Breeding for sustainability

Breeding for sustainability

Reasons for keeping dairy goats in Tanzania, and possible goals for a sustainable breeding program

This research aimed at describing reasons for keeping dairy goats in Tanzania, and possible goals for a sustainable breeding program. Three districts, each representing a unique dairy goat breed population, were selected for the study. The Saanen, Toggenburg and Norwegian were the main dairy goat breeds in Arumeru, Babati, and Mvomero districts, respectively. A total of 125 dairy goat farmers were interviewed. A holistic approach of both quantitative and qualitative research methods was used to study the perceptions of farmers. More milk yield, sale of breeding stock and manure were the highest ranked reasons for keeping dairy goats. The reasons were coherent to the production systems. The three most preferred traits for improvement were milk yield, adaptability and twinning ability. These preferences were absolutely important in the context of the referred production system. Selection of replacement stock, animal identification and performance recording were the main challenges emphasised by farmers. The present study views these challenges as a result of knowledge gaps in animal breeding that require solutions. Based on result findings it is suggested that the milk yield and survival traits should be the primary dairy goat breeding goals. Generally, there are possibilities for developing sustainable dairy goat breeding programs in the surveyed areas given relevant breeding goals are incorporated. The design of simple and manageable dairy goat breeding schemes is necessary.

Leaf protein analyses in order to utilise the leaf shoot of artichoke

The constat growth of the Earth’s population brings with itself a higher demand for food and protein not only in human nutrition but also for the feeding of livestock. Currently, the feed industry is mainly built onseed-based protein, wherethebaseplant is soybean, which is large lycovered by imports in Hungary, similar toother European countries. However, the long-term economically sustainable lifestock breeding demandschanges which has also worked out strategies. An alternative protein sources could be green leafy plants.
 In current work the Jerusalem artichokes as an alternative source of protein was studied, compared to alfalfa as a valuable protein plant. Our results indicate that fiber fraction ofJerusalem artichoke shootswas 34 to 37% after pressing in the autumn period while alfalfa slightly lower values were obtained (30%). On the other hand extracted green leaf protein concentration was higher in alfalfa than in Jerusalem artichoke. Along with this higher protein content could be measured from the leaf protein concentration of alfalfa and almost each amino acids were more, as well comparing to Jerusalem artichoke.
 Overall, the alfalfa proved to be advantageous as expected both in leaf protein extraction efficiency, both regarding the content of the protein in the Jerusalem artichoke. However, considering aminoacid composition and green biomass production, Jerusalem artichokecould be a promisingplant species asplant protein sourceinthefuture.

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria.

The plant growth-promoting rhizobacterium (PGPR) Pseudomonas simiae WCS417r stimulates lateral root formation and increases shoot growth in Arabidopsis thaliana (Arabidopsis). These plant growth-stimulating effects are partly caused by volatile organic compounds (VOCs) produced by the bacterium. Here, we performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis for the ability to profit from rhizobacteria-mediated plant growth-promotion. To this end, 302 Arabidopsis accessions were tested for root architecture characteristics and shoot fresh weight in response to exposure to WCS417r. Although virtually all Arabidopsis accessions tested responded positively to WCS417r, there was a large variation between accessions in the increase in shoot fresh weight, the extra number of lateral roots formed, and the effect on primary root length. Correlation analyses revealed that the bacterially-mediated increase in shoot fresh weight is related to alterations in root architecture. GWA mapping for WCS417r-stimulated changes in root and shoot growth characteristics revealed 10 genetic loci highly associated with the responsiveness of Arabidopsis to the plant growth-promoting activity of WCS417r. Several of the underlying candidate genes have been implicated in important plant growth-related processes. These results demonstrate that plants possess natural genetic variation for the capacity to profit from the plant growth-promoting function of a beneficial rhizobacterium in their rhizosphere. This knowledge is a promising starting point for sustainable breeding strategies for future crops that are better able to maximize profitable functions from their root microbiome.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-016-0442-2) contains supplementary material, which is available to authorized users.

Contrasting patterns of genetic variation in core and peripheral populations of highly outcrossing and wind pollinated forest tree species.

Gene flow tends to have a homogenising effect on a species' background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine-a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species' putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs.

Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

Aim:In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama).Methods:Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software.Results:A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds.Conclusions:The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.

Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Sustainable dairy cattle selection in the genomic era.

Genomic selection offers considerable flexibility to increase genetic trends in dairy cattle breeding. It is also an opportunity for more sustainable breeding, in terms of breeding goal and genetic variability. With a shorter generation interval, there is a big risk of increasing inbreeding if semen dissemination policy of elite bulls is not changed. However, using a large number of young bulls as service bulls and bull sires is a solution for both maximizing genetic trend while reducing inbreeding trend. Female genotyping is a key challenge for within-herd selection but, more importantly, for selection of new traits and for replacement of current reference populations based upon progeny-tested bulls. Genomic selection also opens new avenues for more customized breeding across herds or production systems. A big challenge is to reduce the dependency of genomic predictions on relationship between candidates and the reference population. A strong effort is presently dedicated to integrating genome sequence information into predictions, to improve their accuracy and persistency. In the longer term, further customization of selection will be possible by accounting for G × E interactions. Important developments are also necessary to decrease loss of favourable alleles through genetic drift.

Recurrent selection for wider seedling leaves increases early biomass and leaf area in wheat (Triticum aestivum L.).

The breeding of wheat with greater early vigour has potential to increase water- and nutrient-use efficiency, as well as to improve weed competitiveness to raise crop yields profitably. Given that wheat is inherently conservative in its early growth, a sustained breeding effort was initiated to increase genetically seedling leaf area in developing novel high vigour germplasm. A recurrent selection programme was initiated by intercrossing a genetically diverse set of 28 vigorous wheat lines identified globally. These were intercrossed at random and S1:2 progeny with the largest leaf 1 and 2 widths were intermated to develop new populations for assessment of early growth. This procedure was repeated for up to 60 segregating families per cycle across six cycles over 15 years. Thirty random S1:2 progeny were retained from each cycle and seed-increased together to produce seed for early vigour assessment in multiple sowings. The most vigorous wheat seedlings were identified in later cycles, with some lines producing more than double the leaf area and biomass of elite commercial wheat varieties. Phenotypic selection for greater leaf width was associated with a realized significant (P<0.01) linear increase per seedling of 0.41 mm per cycle (+7.1%) for mean leaf width, and correlated linear increases in total leaf area and biomass of 4.48 cm(2) per cycle (+10.3%) and 10.8 mg per cycle (+5.3%), respectively. Genetic gains in widths of leaves 2 (+8.4%) and 3 (+11.5%) were significantly (P<0.01) greater than for leaf 1 (+5.3%). Selection for greater leaf width was associated with linear increases in coleoptile tiller leaf area, small curvilinear increases in leaf 1 length, and reductions in numbers of leaves and mainstem tillers. Genetic variances were large and heritabilities high for leaf width and total leaf area in each cycle, but reduced linearly in size with selection across cycles. Coupling diverse germplasm with a simple, inexpensive, and repeatable selection process has confirmed the value of recurrent selection in developing uniquely vigorous wheat germplasm for use as parents in commercial breeding.