Random Mating Research Articles

The genetic legacy of fragmentation and overexploitation in the threatened medicinal African pepper-bark tree, Warburgia salutaris

The pepper-bark tree (Warburgia salutaris) is one of the most highly valued medicinal plant species worldwide. Native to southern Africa, this species has been extensively harvested for the bark, which is widely used in traditional health practices. Illegal harvesting coupled with habitat degradation has contributed to fragmentation of populations and a severe decline in its distribution. Even though the species is included in the IUCN Red List as Endangered, genetic data that would help conservation efforts and future re-introductions are absent. We therefore developed new molecular markers to understand patterns of genetic diversity, structure, and gene flow of W. salutaris in one of its most important areas of occurrence (Mozambique). In this study, we have shown that, despite fragmentation and overexploitation, this species maintains a relatively high level of genetic diversity supporting the existence of random mating. Two genetic groups were found corresponding to the northern and southern locations. Our study suggests that, if local extinctions occurred in Mozambique, the pepper-bark tree persisted in sufficient numbers to retain a large proportion of genetic diversity. Management plans should concentrate on maintaining this high level of genetic variability through both in and ex-situ conservation actions.

Proximate mechanisms responsible for random mating by size in the Himalayan toad Duttaphrynus himalayanus

Abstract Exploring the mechanisms that affect mating pattern with respect to body size has implications for understanding the evolution of sexual selection. Theory predicts that the absence of a relationship between female body size and fecundity, unbiased operational sex ratio, and a short breeding season will lead to random mating by body size in anuran amphibians. We tested these predictions in the Himalayan toad Duttaphrynus himalayanus inhabiting southeastern Tibet. Our study did not detect any correlation between female body size and number of eggs laid, nor was there a significant difference in the sex ratio of toads captured from the breeding site. In addition, the toads were reproductive for only a short period, from late April to early May (typical of an explosively breeding species). As expected, we detected a weak but not significant relationship between body size of amplexing males and females. Our results revealed no apparent size-assortative pairing in the study population of the Himalayan toad and may contribute to an increasing body of literature on mating patterns in relation to body size in animals with indeterminate growth.

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = − 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species’ genetic variation or limit the species’ ability to respond to further selection pressure.

Outcrossing Mating System of the Early-Divergent Moonwort Fern (Botrychium lunaria, Ophioglossaceae) Revealed in the European Alps

Premise of research. Vascular plants depend on sexual recombination for generating new genetic variability to meet environmental needs. Nevertheless, members of the early-divergent fern genus Botrychium (Ophioglossaceae) typically maintain gametophytic selfing and show strong inbreeding within populations. To explain this evolutionary anomaly, the existence of previous or current but undiscovered outcrossing, genetically rich precursors of the existing genetically depauperate taxa, has been hypothesized.Methodology. Using allele expression at 13 independently assorting enzyme loci, we compared allelic diversity and levels of heterozygosity in 471 B. lunaria individuals across 16 populations in the Alps and Jura Mountains of Switzerland. We examined habitat characteristics influencing mating systems and investigated population genetic structure on the basis of a discriminant analysis of principal components (DPAC) and a graph-theoretic framework. We tested the pattern of isolation by distance and explored the biological processes favoring or limiting spore dispersal at a regional scale.Pivotal results. We found high genetic diversity within and among populations and similar observed heterozygosity (HO) and expected heterozygosity (HS) across loci (HO = 0.020–0.450 and HS = 0.040–0.590, respectively). Estimates of HO (0.050–0.272) were lower than those of HS (0.144–0.305) across individuals, indicating a weak deficit in heterozygotes. Mean values of departure (D) from expected heterozygosity were close to what would be expected with random mating (DL=0.061 and DP=0.059 across loci and populations, respectively). The mean inbreeding coefficient (FIS) was low (FIS=0.247), and the overall genetic differentiation (FST) was moderate (global FST=0.083).Conclusions. Together, the DAPC and the population graph revealed a complex population genetic structure and weak genetic differentiation, with substantial gene flow among most populations. One population (Arosa), sampled from a site recently released from permafrost, demonstrated a probable founder effect not correlated with geographical isolation. The topology of the population graph identified three subgroups with several key populations (Bosco Gurin, Chandolin Low, Grand St. Bernard, San Bernardino, and Val Roseg) that maintained genetic connectivity of populations from distant locations.

Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis

Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.

Kin-Mediated Male Choice and Alternative Reproductive Tactics in Spider Mites.

Simple SummaryEvolutionary-grounded theories predict that any mating-related behavior should be influenced by the degree of genetic relatedness between the involved interactants. Close genetic relatedness may have beneficial and detrimental effects on evolutionary fitness. To optimize these trade-offs, mates should be able to discriminate kin and non-kin and adjust their behaviors accordingly. Here, we assessed kin-dependent mate choice and adjustment of alternative reproductive tactics (ARTs) in male spider mites. Our experiments suggest that male spider mites can assess kinship of rivals and prospective mates. Mate choice and expression of ARTs (fighting versus sneaking) were driven by direct and indirect fitness benefits arising from the degree of kinship of available mates and rival males competing for access to females. Depending on the social context (choice vs. no-choice, w/wo competition) and achievable fitness benefits, males seemed to use novelty as absolute decision rule and/or comparative evaluation in mate choice. Close kinship among rivals mitigated the males’ fighting propensity and favored adoption of the sneaking tactic. Overall, our study highlights kin-mediated plasticity in male choice and expression of ARTs and emphasizes the importance to consider different contexts and inclusive fitness benefit/cost trade-offs when interpreting mating preferences.Optimal outbreeding and kin selection theories state that the degree of kinship is a fundamental determinant in any mating system. However, the role of kinship in male choice and alternative reproductive tactics (ARTs) is poorly known. We assessed the influence of kinship on male choice and expression of ARTs in two populations of two-spotted spider mites Tetranychus urticae. Male spider mites guard premature females, which is an indicator of mate choice, and may conditionally adopt fighting or sneaking tactics to secure access to females. Males competing with kin or non-kin were offered one kin or non-kin female (experiment 1) and single males were presented a choice of kin and non-kin females (experiment 2). Under kin competition, males of both populations were more prone to guard non-kin than kin females at a 3:1 fighter:sneaker ratio. Under non-kin competition, all males were fighters. Under no-choice, males used novelty as indicator of genetic dissimilarity, serving as absolute decision rule for outbreeding. Under choice, comparative evaluation allowed males to preferentially guard females with higher reproductive potential. Overall, our study suggests that male spider mites can assess kinship of rivals and prospective mates. Kin discrimination allows adaptive, context-specific non-random mating preference and adjustment of ARTs.

Frequency of Blood Types A, B and AB in a Population of Non-Pedigree Domestic Cats from Central Italy.

Simple SummaryThis study aimed to evaluate the frequency of AB blood groups in non-pedigree domestic cats in Central Italy. The presence of natural alloantibodies in the feline blood group system can cause life-threatening transfusion reactions due to mismatched transfusion and, depending on the parents’ blood type, can also account for hemolytic reactions in newborn kittens. Based on the frequency of the AB blood groups found in the 483 cats studied, a potential risk (6.5%) of acute hemolytic transfusion or neonatal reactions was calculated. Therefore, determining the blood group in non-pedigree domestic cats from Central Italy before transfusion is strongly recommended, as has been reported for other geographical areas. Moreover, particular attention should be paid to the mating of non-purebred cats.Blood transfusion reactions and neonatal isoerythrolysis are common events in the feline population due to the presence of natural alloantibodies in the AB blood group system. It is known that the frequency of feline blood types varies according to the geographic region and breed. Therefore, the aims of this study were to investigate the frequency of AB blood groups in non-pedigree domestic cats in Central Italy and estimate the risk of a life-threatening transfusion reaction and neonatal isoerythrolysis, caused by mismatched transfusion or incompatible random mating, respectively. The AB blood group was determined on non-pedigree domestic feline patients and potential blood donors submitted at the Veterinary Teaching Hospitals of the Universities of Teramo (Abruzzo Region, Teramo, Italy) and Perugia (Umbria Region, Teramo, Italy), and visited at veterinary practitioners in Rome (Lazio Region, Teramo, Italy) using commercial immunochromatographic cartridges and commercial agglutination cards. There were four hundred and eighty-three cats included in the study. The frequencies of the blood types were: 89.9% type A, 7.0% type B, and 3.1% type AB. The probability of an acute hemolytic transfusion reaction or a neonatal isoerythrolysis was 6.5%. Although the frequency of type B in non-pedigree domestic cats living in Central Italy was relatively low, to reduce the risk of fatal transfusion reactions, blood group typing is recommended before each transfusion.

Does Functionality Condition the Population Structure and Genetic Diversity of Endangered Dog Breeds under Island Territorial Isolation?

Simple SummaryEarly references to Ca de Rater and Ca de Bestiar endangered autochthonous breeds were witnesses to their exceptional ratting/pet and shepherding/guard skills for centuries. Studbooks or associations promote an increase in the number of effectives and their genealogies. Genetic diversity parameters were evaluated along the history of definition of both dog breeds. Guard or hunting purposes condition an increased registration of genealogical information. Hunting animals have more complete genealogies and need more time to select breeding animals. Male guard dogs are preferred over females due to their suitability for guarding. Selection for performance acts as a diversity promoter and breeding policy driver. The uses or purposes for which certain breeds were selected condition the genetic diversity evolution of endangered breeds, even if these share the same geographic isolation conditions.Despite the undefinition of the origins of Ca de Rater (CR) and Ca de Bestiar (CB) dogs, references to these endangered autochthonous breeds highlighted their ratting/pet and shepherding/guard skills for centuries. Genealogical historical records were traced back to founders. Founder number in the reference population (146 and 53 for CR and CB, respectively), historical and reference maximum generations traced (eight and seven for CR and CB, respectively), and historical average number of complete generations (1.04 for both breeds) were determined. Structure assessment revealed the existence of subpopulations regarding criteria such as breeders (75 and 17), breeder location (32 and eight), owners (368 and 198), and owner location (73 and 51) for CR and CB, respectively. Average inbreeding (F) within breed subpopulations ranged from 0.27–1.20% for CB breeders and the rest of subpopulation criteria for both breeds, respectively, except for CB owners and owner location. F ranged from 0.27–1.41% for CB historical population and CR current population, respectively. The study of genetic diversity revealed a relatively similar genetic background between subpopulations. Average coancestry between and within breeds suggested a similar evolutionary process. However, Mann–Whitney U test determined significant differences for diversity parameters (F, ΔR, coancestry, nonrandom mating degree, maximum, complete, and equivalent generations, ΔF, and genetic conservation index) between breeds and their functionalities. Conclusively, functionality in dog breeds may determine the genetic diversity evolution of endangered breeds, even when these share the same geographic isolation conditions.

Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population.

A multiparental random mating population used in sorghum breeding is amenable for the detection of QTLs related to tropical soil adaptation, fine mapping of underlying genes and genomic selection approaches. Tropical soils where low phosphorus (P) and aluminum (Al) toxicity limit sorghum [Sorghum bicolor (L.) Moench] production are widespread in the developing world. We report on BRP13R, a multiparental random mating population (MP-RMP), which is commonly used in sorghum recurrent selection targeting tropical soil adaptation. Recombination dissipated much of BRP13R's likely original population structure and average linkage disequilibrium (LD) persisted up to 2.5Mb, establishing BRP13R as a middle ground between biparental populations and sorghum association panels. Genome-wide association mapping (GWAS) identified conserved QTL from previous studies, such as for root morphology and grain yield under low-P, and indicated the importance of dominance in the genetic architecture of grain yield. By overlapping consensus QTL regions, we mapped two candidate P efficiency genes to a ~ 5Mb region on chromosomes 6 (ALMT) and 9 (PHO2). Remarkably, we find that only 200 progeny genotyped with ~ 45,000 markers in BRP13R can lead to GWAS-based positional cloning of naturally rare, subpopulation-specific alleles, such as for SbMATE-conditioned Al tolerance. Genomic selection was found to be useful in such MP-RMP, particularly if markers in LD with major genes are fitted as fixed effects into GBLUP models accommodating dominance. Shifts in allele frequencies in progeny contrasting for grain yield indicated that intermediate to minor-effect genes on P efficiency, such as SbPSTOL1 genes, can be employed in pre-breeding via allele mining in the base population. Therefore, MP-RMPs such as BRP13R emerge as multipurpose resources for efficient gene discovery and deployment for breeding sorghum cultivars adapted to tropical soils.

Assessment of Genetic Diversity in Azerbaijani Buffalo Population in Iran Based on Runs of Homozygosity Stretches

Quantifying human, plant and livestock inbreeding has been an important goal of evolutionary biologists and agricultural scientists for nearly a century. Comprehensive identification of the breed characteristics is a critical factor for the effective management of farm animal genetic resources. The objective of this study was to estimate inbreeding coefficients derived from runs of homozygosity islands from 243 Iranian Azerbaijani buffalos using dense SNP markers (Axiom® Buffalo Genotyping 90K). After quality control, 62,141 SNP markers remained for computation of inbreeding coefficients. The amount of estimated inbreeding coefficient using four methods including genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation of uniting gametes (FUNI) and FIS was similar (0.026) and it was estimated 0.0163 using Run of homozygosity procedure. Low levels of FROH in Azerbaijan buffalo population can be due to the traditional rural breeding system, random mating, high recombination rate and small population of ancestors.

Maternal-fetal genetic interactions, imprinting, and risk of placental abruption

Background: Maternal genetic variations, including variations in mitochondrial biogenesis (MB) and oxidative phosphorylation (OP), are associated with placental abruption (PA). However, the role of maternal-fetal genetic interactions (MFGI) and parent-of-origin (imprinting) effects in PA remain unknown. Objective: To investigate MFGI in MB-OP, and imprinting effects in relation to risk of PA. Methods: Among Peruvian mother-infant pairs (503 PA cases and 1052 controls), independent single nucleotide polymorphisms (SNPs), with linkage-disequilibrium coefficient <0.80, were selected to characterize genetic variations in MB-OP (78 SNPs in 24 genes) and imprinted genes (2713 SNPs in 73 genes). For each MB-OP SNP, four multinomial models corresponding to fetal allele effect, maternal allele effect, maternal and fetal allele additive effect, and maternal-fetal allele interaction effect were fit under Hardy-Weinberg equilibrium, random mating, and rare disease assumptions. The Bayesian information criterion (BIC) was used for model selection. For each SNP in imprinted genes, imprinting effect was tested using a likelihood ratio test. Bonferroni corrections were used to determine statistical significance (p-value < 6.4e-4 for MFGI and p-value < 1.8e-5 for imprinting). Results Abruption cases were more likely to experience preeclampsia, have shorter gestational age, and deliver infants with lower birthweight compared with controls. Models with MFGI effects provided improved fit than models with only maternal and fetal genotype main effects for SNP rs12530904 (p-value = 1.2e-04) in calcium/calmodulin-dependent protein kinase [CaM kinase] II beta (CAMK2B), and, SNP rs73136795 (p-value = 1.9e-04) in peroxisome proliferator-activated receptor-gamma (PPARG), both MB genes. We identified 320 SNPs in 45 maternally-imprinted genes (including potassium voltage-gated channel subfamily Q member 1 [KCNQ1], neurotrimin [NTM], and, ATPase phospholipid transporting 10 A [ATP10A]) associated with abruption. Top hits included rs2012323 (p-value = 1.6E-16) and rs12221520 (p-value1.3e-13) in KCNQ1, rs8036892 (p-value = 9.3E-17) and rs188497582 in ATP10A, rs12589854 (p-value = 2.9E-11) and rs80203467 (p-value = 4.6e-11) in maternally expressed 8, small nucleolar RNA host (MEG8), and rs138281088 in solute carrier family 22 member 2 (SLC22A2) (p-value = 6.8e-9). Conclusions We identified novel PA-related maternal-fetal MB gene interactions and imprinting effects that highlight the role of the fetus in PA risk development. Findings can inform mechanistic investigations to understand the pathogenesis of PA.

Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

Growth and reproductive performances of Hilly Brown Bengal goat under semi-intensive management condition at Naikhongchari hilly areas of Bangladesh

The objective of the study was to evaluate the growth and reproductive performances of Hilly Brown Bengal (HBB) goats of different generations and conducted at Naikhongchari Regional Station Research Farm of Bangladesh Livestock Research Institute. Goats were reared in a plastic slated floor under semi-intensive system and were allowed to graze for 6-7 hours per day. Animals were given a concentrate mixture containing 17% CP, 11 MJ ME/kg DM provided twice daily in the morning and evening at the rate of 1% of their body weight. All goats were kept separately according to sex and age groups to avoid random mating. Natural mating program was performed to improve the economically important traits. Goats were de-wormed and diping on regular intervals and only PPR vaccine was given at the age of 2 months. Data on productive, reproductive and disease incidence of goat were recorded regularly and were analyzed. Results showed that Kid Birth Weight of HBB goats were significantly (P&lt;0.01) differ among generations. Birth weight of G3 (1.21±0.013 kg) was higher than G5, G4, G2 and G1 (1.11±0.01 kg). Goat body weight of 3, 6 and 9 months age were non-significant among generations. The age and weight at first conception were significantly (p&lt;0.05) differ among generation. Age at first conception was lower of G4 (301.57±9.06 days) and higher of G1 (259.80±18.87 days) but body weight at first conception of G1 (12.23±0.47 kg) was higher and G4 was lower (10.65±0.52 kg). Age at first kidding, gestation length and kidding interval was not significant (P&gt;.05) effect on generations. Parity had no significant (P&gt;.05) effect on kid birth weight but significantly (p&lt;0.01) differ of Kid litter weight and litter size. According to birth type single kid was highest birth weight (1.21±0.08 kg) than double kid followed by triplet and quadruplet. Mortality percentage of HBB kids at the age of 0-90 days were 13.08±0.23%. It may be concluded that kid birth weight, age and weight at first conception of HBB goat were significantly (P&lt;.05) affected on generation but age at first kidding, gestation length and kidding interval were non significantly (P&lt;.05) affected.&#x0D; Asian Australas. J. Biosci. Biotechnol. 2020, 5 (2), 72-77

Many loci make light work: High individual diversity despite low population diversity and random mating at class I MHC in a Critically Endangered island songbird.

Multi-cellular organisms are under constant attack from parasites, making immune defence a critical aspect of fitness. In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the breadth of pathogens to which individuals can respond. Having many MHC alleles can confer better protection against infectious disease, and balancing selection at MHC is widespread. Indeed, MHC loci are famously variable, with some populations harbouring thousands of alleles (Biedrzycka et al., 2018; Robinson, Soormally, Hayhurst, & Marsh, 2016). MHC has also long fascinated behavioural ecologists because mate choice-for example, preferring MHC-dissimilar partners-may amplify the effects of natural selection (Penn & Potts, 1999). But despite keen interest in the evolutionary ecology of MHC, extensive duplication (Minias, Pikus, Whittingham, & Dunn, 2019) has made these genes challenging to study. In a From the Cover article in this issue of Molecular Ecology, Stervander, Dierickx, Thorley, Brooke, and Westerdahl (2020) characterizes class I MHC in a Critically Endangered songbird, relating genotype to mate choice and survivorship. By inferring copy number and patterns of allelic co-segregation, the authors pave the way to elucidating the genomic architecture of MHC in this bottlenecked population. These insights help reconcile apparently counterintuitive findings: no effect of MHC genotype on mate choice or survival, and high MHC diversity within individuals despite low diversity at the population level. The latter finding is cause for optimism regarding conservation prospects. Moreover, these results suggest that ancient duplication events can have longstanding effects on the adaptive landscapes of natural and sexual selection.

Genetic consequences of social structure in the golden-crowned sifaka

Many species are structured in social groups (SGs) where individuals exhibit complex mating strategies. Yet, most population genetic studies ignore SGs either treating them as small random-mating units or focusing on a higher hierarchical level (the population). Empirical studies acknowledging SGs have found an overall excess of heterozygotes within SGs and usually invoke inbreeding avoidance strategies to explain this finding. However, there is a lack of null models against which ecological theories can be tested and inbreeding avoidance quantified. Here, we investigate inbreeding (deviation from random mating) in an endangered forest-dwelling pair-living lemur species (Propithecus tattersalli). In particular, we measure the inbreeding coefficient (FIS) in empirical data at different scales: SGs, sampling sites and forest patches. We observe high excess of heterozygotes within SGs. The magnitude of this excess is highly dependent on the sampling scheme: while offspring are characterised by a high excess of heterozygotes (FIS < 0), the reproductive pair does not show dramatic departures from Hardy–Weinberg expectations. Moreover, the heterozygosity excess disappears at larger geographic scales (sites and forests). We use a modelling framework that incorporates details of the sifaka mating system but does not include active inbreeding avoidance mechanisms. The simulated data show that, although apparent “random mating” or even inbreeding may occur at the “population” level, outbreeding is maintained within SGs. Altogether our results suggest that social structure leads to high levels of outbreeding without the need for active inbreeding avoidance mechanisms. Thus, demonstrating and measuring the existence of active inbreeding avoidance mechanisms may be more difficult than usually assumed.

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

Key MessagePaternity assignment and genome-wide association analyses for fertility were applied to aThinopyrum intermediumbreeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes.In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.

Genetic monitoring of translocated plant populations in practice.

Plant translocations allow the restoration of genetic diversity in inbred and depauperate populations and help to prevent the extinction of critically endangered species. However, the successes of plant translocations in restoring genetically viable populations and the possible associated key factors are still insufficiently evaluated. To fill this gap, we carried out a thorough genetic monitoring of three populations of Arnica montana that were created or reinforced by the translocation of plants obtained from seeds of two large natural source populations from southern Belgium. We genotyped nine microsatellite markers and measured fitness quantitative traits over two generations (transplants, F1 seed progeny and newly established F1 juveniles). Two years after translocation, the genetic restoration had been effective, with high genetic diversity and low genetic differentiation across generations, extensive contemporary pollen flow, admixture between seed sources in the F1 generation and recruitment of new individuals from seeds. We detected site, seed source and maternal plant effects on plant fitness. The results also suggest that phenotypic plasticity may favour short-term individual survival and long-term adaptive capacity and enhance the evolutionary resilience of the populations to changing environmental conditions. We found no sign of heterosis or outbreeding depression at early life stages in the F1 generation. Our findings emphasize the importance of the translocation design (700 transplants of mixed sources, planted at high density) as well as the preparatory site management for the successful outcome of the translocations, which maximized flowering, random mating, and recruitment from seeds in the first years after translocation.

Identification of a new potential native Indian cattle breed by population differentiation based on microsatellite markers.

India has a rich heritage of rearing cattle where farmers selected native cattle suitable to their local agro-ecological conditions for centuries. It is reflected in 50 indigenous breeds of cattle, besides many lesser known populations not explored so far. It is the need of the hour to characterize such populations to have prudent improvement and conservation options. Thus, present study was carried out to assess the genetic diversity and relationship between an unexplored local cattle population (Kathani) and four established cattle breeds of adjoining area (Gaolao, Kosali, Ongole and Motu) by using 20 FAO recommended microsatellite markers. High variability was recorded in the Kathani population with a total of 198 alleles that varied between 5 (ILSTS11, TGLA22, INRA05) and 17 (ILSTS34) with a mean of 9.9 ± 0.73. The average observed heterozygosity (Ho) was 0.658 ± 0.054. Heterozygote deficiency was not significant (FIS = 0.029 ± 0.063) indicating random mating prevalent across this population. Mean estimates of observed number of alleles and heterozygosity over all the loci and five populations were 9.73 ± 0.421 and 0.617 ± 0.022, respectively. In the overall populations, the homozygote excess (FIT) of 0.293 ± 0.032, was partly due to the homozygote excess within breeds (FIS = 0.121 ± 0.025) and to a larger extent due to high (0.05 < FST < 0.15) genetic differentiation among them (FST = 0.195 ± 0.029). Substantial pairwise Nei's genetic distance and high population differentiation indicated towards separate genetic identity of Kathani cattle. The analysis of genetic structure based on Bayesian approach indicated that the most probable number of clusters is five confirming definitive genetic differentiation among all the popultions. Entire analysis showed that a significant amount of genetic variation is maintained in Kathani, a lesser known cattle population that is distinct from the recognized breeds in the proximity. As this autochthonous cattle plays role in the economic sustainability of a marginal and disadvantaged area, it is important to preserve and develop its breeding.

Intra- and interspecific sexual isolation in two sibling species of Drosophila: D. ananassae and D. pallidosa

We tested intraspecific as well as interspecific sexual isolation in two sibling species of Drosophila: D. ananassae and D. pallidosa by the multiple-choice technique. The results indicate significant deviations from random mating in both intraspecific as well as interspecific crosses, which demonstrates the existence of strong sexual isolation. Differences in mating propensity in different strains of both the species may be hypothesized as the primary cause behind intraspecific sexual isolation. However, this result was not expected because D. pallidosa is an endemic species that exhibits a greater degree of intraspecific isolation as compared to its cosmopolitan sibling species D. ananassae. Further, both the species show a considerable degree of sexual isolation. We discuss the evolutionary status of both the sibling species in light of these results.

Recombination disequilibrium in ideal and natural populations

Following Hardy-Weinberg disequilibrium (HWD) occurring at a single locus and linkage disequilibrium (LD) between two loci in generations, we here proposed the third genetic disequilibrium in a population: recombination disequilibrium (RD). RD is a measurement of crossover interference among multiple loci in a random mating population. In natural populations besides recombination interference, RD may also be due to selection, mutation, gene conversion, drift and/or migration. Therefore, similarly to LD, RD will also reflect the history of natural selection and mutation. In breeding populations, RD purely results from recombination interference and hence can be used to build or evaluate and correct a linkage map. Practical examples from F2, testcross and human populations indeed demonstrate that RD is useful for measuring recombination interference between two short intervals and evaluating linkage maps. As with LD, RD will be important for studying genetic mapping, association of haplotypes with disease, plant breading and population history.