Dynamics of Correlated Genetic Systems. V. Rates of Decay of Linkage Disequilibria in Experimental Populations of DROSOPHILA MELANOGASTER

The dynamic behavior of four-locus gametic frequency distributions was studied in five replicate cage populations of Drosophila melanogaster for up to 50 generations. The joint frequency distributions were resolved into gene frequencies and various disequilibrium measures. In addition, F statistics for marginal single-locus genotypic frequency distributions were followed through time. The gene frequency, disequilibrium and F statistics were obtained for four chromosome 3 enzyme marker loci [isocitrate dehydrogenase (3–27.1), esterase-6 (3–36.8), phosphoglucomutase (3–43.4) and esterase-C (3–49.0)]. The initial structure of the experimental populations featured random mating proportions, and two complementary gametic types with respect to the marker loci, thus assuring complete pairwise linkage disequilibrium among the markers.——The experimental results indicate: (1) the between-replicate variance in gene frequency varied substantially among loci, with isocitrate dehydrogenase showing the greatest between-replicate variance, and esterase-C the least. (2) The F statistics initially were strongly negative but decayed to the neighborhood of zero for all marker loci except esterase-C. The rate at which the F statistics approached zero varied among the marker loci, indicating substantial differences in the distribution of selective effects along the chromosome. The centromeric region, marked by esterase-C, shows the strongest selective effects. (3) The rate of decay of linkage disequilibrium was much faster than expected for pairs of neutral loci, averaging 1.82 times the neutral rate over all replicates and pairs of loci. This acceleration, which was observed for all six pairwise combinations of loci, was interpreted as resulting from the interaction between selection and recombination. Our experimental results are consistent with many investigations of linkage disequilibrium in natural populations of Drosophila melanogaster that show little or no disequilibrium among enzyme loci. (4) A fortuitous contamination of two cages revealed an apparent regulatory interaction between the migrant and nonmigrant chromosomes at the esterase-C locus. The migrant chromosomes were very rapidly absorbed into the recipient populations, despite this interaction. This result suggests that the dynamics of migration in populations may be phenomenologically richer than anticipated by simple theory.     

Inheritance of Semidwarfism in Rice, ORYZA SATIVA L

The inheritance of plant height was investigated in a ten-parent diallel cross of diverse rice cultivars. Parents included two tall japonica lines and eight semidwarf lines. Data from parent, F₁, F₂ , and F₃ generations indicated that the majority of height variation among the ten parents could be accounted for by three major genes with additive loci effects. D51, 72/2234–11, and G33 (derived from the known major-gene indica semidwarf Dee-geo-woo-gen) all were found to possess an allelic, partially recessive semidwarfing gene (sd₁). Additional semidwarfing genes were detected in D66 (sd₂, fully recessive) and in CI 9858 (sd₃, partially to fully recessive). Relative magnitudes of additive effects were sd₁ > sd₂ ≥ sd₃. Hokuriki 76, Tedoriwase, and IV 29–4 were found to be dwarfed by a multiple-gene system. Hayman-Jinks diallel cross analysis on parent and F₁ information (1974 and 1975) and on parent and F₂ information demonstrated the presence of significant additive and dominance variation, but epistasis was not detected. A preponderance of dominant alleles with partial dominance for increased plant height was observed. Since diallel statistics reflect properties of genes with larger effects, the genetic model proposed from segregation analysis was in substantial agreement with predictions of the Hayman-Jinks analysis.     

Allozyme Segregation Ratios in the Interspecific Cross CUCURBITA MAXIMAxC. ECUADORENSIS Suggest That Hybrid Breakdown Is Not Caused by Minor Alterations in Chromosome Structure

The parentals of the interspecific cross Cucurbita maxima x C. ecuadorensis had different isozyme phenotypes for 12 enzyme systems. Characterization of the systems demonstrated that the expression and intracellular distribution of the isozymes were similar to those in other plant taxa; however, a considerable number of duplicate loci were identified, indicative of a polyploid ancestry for Cucurbita. Genetic analysis provided evidence for 20 loci segregating in F₂ and backcross populations. Five linkage groups were identified, consisting of the loci Aat-mb – – Mdh-m2; Gal-1 – – Gal-2; Aat-p2 – – Gpi-c2; Acp-1 – – Pgm-c2 – – Pgm-p; and Est-1 – – Tpi-c2. Significant deviations from Mendelian segregation ratios were observed in 14% of the data sets for individual loci. However, these instances were scattered among the loci, no single locus consistently displaying skewed ratios. Recombination frequencies between linked loci were similar to those observed in intraspecific crosses, and the ratio of heterozygous to homozygous genotypes in backcross populations was very close to one. These results suggest that small differences in chromosome structure were not the major cause of the loss of fertility observed in F₂ and backcross populations.     

Transmission dynamics of heritable silencing induced by double-stranded RNA in Caenorhabditis elegans

Heritable silencing effects are gene suppression phenomena that can persist for generations after induction. In the majority of RNAi experiments conducted in Caenorhabditis elegans, the silencing response results in a hypomorphic phenotype where the effects recede after the F₁ generation. F₂ and subsequent generations revert to the original phenotype. Specific examples of transgenerational RNAi in which effects persist to the F₂ generation and beyond have been described. In this study, we describe a systematic pedigree-based analysis of heritable silencing processes resulting from initiation of interference targeted at the C. elegans oocyte maturation factor oma-1. Heritable silencing of oma-1 is a dose-dependent process where the inheritance of the silencing factor is unequally distributed among the population. Heritability is not constant over generational time, with silenced populations appearing to undergo a bottleneck three to four generations following microinjection of RNA. Transmission of silencing through these generations can be through either maternal or paternal gamete lines and is surprisingly more effective through the male gametic line. Genetic linkage tests reveal that silencing in the early generations is transmitted independently of the original targeted locus, in a manner indicative of a diffusible epigenetic element.     

Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice

Grain length is an important quantitative trait in rice (Oryza sativa L.) that influences both grain yield and exterior quality. Although many quantitative trait loci (QTLs) for grain length have been identified, it is still unclear how different alleles from different QTLs regulate grain length coordinately. To explore the mechanisms of QTL combination in the determination of grain length, five mapping populations, including two F₂ populations, an F₃ population, an F₇ recombinant inbred line (RIL) population, and an F₈ RIL population, were developed from the cross between the U.S. tropical japonica variety ‘Lemont’ and the Chinese indica variety ‘Yangdao 4’ and grown under different environmental conditions. Four QTLs (qGL-3-1, qGL-3-2, qGL-4, and qGL-7) for grain length were detected using both composite interval mapping and multiple interval mapping methods in the mapping populations. In each locus, there was an allele from one parent that increased grain length and another allele from another parent that decreased it. The eight alleles in the four QTLs were analyzed to determine whether these alleles act additively across loci, and lead to a linear relationship between the predicted breeding value of QTLs and phenotype. Linear regression analysis suggested that the combination of eight alleles determined grain length. Plants carrying more grain length-increasing alleles had longer grain length than those carrying more grain length-decreasing alleles. This trend was consistent in all five mapping populations and demonstrated the regulation of grain length by the four QTLs. Thus, these QTLs are ideal resources for modifying grain length in rice.     

Extensive heterozygosity at three enzyme loci in hybrid sunfish populations

Hybrid populations of sunfishes were produced in two different ponds, and the frequencies of allelic isozyme phenotypes were determined for three enzyme systems—malate dehydrogenase (NAD), esterases, and tetrazolium oxidase—in order to estimate the extent of heterozygosity at four different genetic loci. Interspecific F₁ hybrid fry (red-ear male × bluegill female) were produced in vitro. These fry were stocked in ponds at the free-swimming stage. When 1 year old, the F₁ hybrids produced a large F₂ hybrid population. Successful hybrid reproduction occurred each year thereafter. In one pond, a 1-year-old F₂ population exhibited all three isozyme phenotypes (red-ear, F₁, bluegill) at most loci in the approximate ratio of the 1:2:1 expected. In a second pond, 5-year-old individuals of the F₂ generation were morphologically like the F₁ and were all heterozygous for the enzyme loci studied. This unusual degree of heterozygosity in the older F₂ population appeared to be the result of differential survival of mature heterozygous individuals and not the result of early embryonic lethality. The increased heterozygosity at these unlinked loci was assumed to reflect the condition at other genetic loci in the F₂ hybrids. Several possible mechanisms are advanced to explain this apparent heterosis.This research was supported by NSF grant GB-16425 (G.S.W.) and by funds from the Illinois Natural History Survey (W.F.C.).     

EVIDENCE FOR AN EXTREME BOTTLENECK IN A RARE MEXICAN PINYON: GENETIC DIVERSITY,DISEQUILIBRIUM, AND THE MATING SYSTEM IN PINUS MAXIMARTINEZII

Maxipiñon (Pinus maximartinezii Rzedowski), which is confined to a single population of approximately 2000 to 2500 mature trees, covers about 400 ha in southern Zacatecas, Mexico. Genetic diversity measured by expected heterozygosity was 0.122, which is moderate for pines. However, percentage polymorphic loci was low, 30.3%. The fixation index (F) of 0.081 indicated only slight heterozygote deficiency. Mating system analysis indicated a significant but low level of selling; the multilocus outcrossing rate, t_m, was 0.816. The mean of single locus estimates, t_s, was smaller (0.761), perhaps suggesting mating among relatives, although the difference between t_m and t_s was not statistically significant. The most striking features of maxipiñon's genetic structure were that no polymorphic locus had more than two alleles and most alleles at polymorphic loci were at intermediate frequencies. This is in contrast to other pines, which often have three to five or more alleles at some loci and in which the distribution of allele frequencies is U-shaped, most alleles being present at frequencies less than 10% or greater than 90%. A population with only two alleles per locus and at intermediate frequencies could occur if the population had been reduced to an extreme bottleneck and then expanded rapidly before random drift modified allele frequencies. A novel origin from a hybridization event would also explain the results. Significant gametic disequilibrium was detected at several pairs of loci in both maternal and paternal gametes. The presence of disequilibrium is in agreement with an origin from an extreme bottleneck, perhaps even a single seed. Furthermore, it demands that the event be relatively recent. The number of generations, as calculated from the observed mean disequilibrium, suggested that maxipiñon derived from an extreme bottleneck four to five generations ago, which is less than 1000 years in this species.     

Genetic diversity and relatedness in different generations of the Siberian crane (Grus leucogeranus Pallas) captive population

Eight variable microsatellite loci were analyzed in terms of studying the genetic structure of different generations of a captive population of a rare endemic Russian species, the Siberian crane (Grus leucogeranus Pallas). It was shown that the founding population of natural origin (15 birds) is characterized by high genetic diversity (N _A = 6.625, H _O = 0.767, H _E = 0.731) and a lack of relatedness (R = ?0.079). In the total sample of descendents of the founders (122 individuals from generations F₁, F₁/F₂, F₁/F₃, F₂, F₂/F₃), this characteristic level of genetic variation is being maintained; however, we observed a decrease in allelic richness in some generations (F₁/F₂, F₁/F₃, F₂). We found a low level of relatedness in the sample of descendents of the founders (F₁, F₁/F₂, F₁/F₃), while the relatedness was maximal (R = 0.302) in the descendents of the breeders of the first generation. A small sample of breeders related to each other of generations F₁ and F₂ (eight birds) does not represent the entire gene pool of the founders of the Siberian Crane captive population. In view of this, we discuss the need to form a new genetically heterogeneous generation of breeders that would also include Siberian Cranes from the almost extinct Western Siberian population.     

Genetic mapping in maize with hybrid progeny across testers and generations: plant height and flowering

DNA markers were used to identify quantitative trait loci (QTLs) for plant height, ear height, and three flowering traits in hybrid progeny of two generations (F_2:3, F_6:8) of lines from a Mo17×H99 maize population. For both generations, testcross (TC) progeny were developed by crossing the lines to three inbred testers (B91, A632, B73). The hybrid progeny from the two generations were evaluated at the same locations but in different years as per an early generation testing program. QTLs were identified within each TC population and for mean testcross (MTC) performance. Overall, more QTLs were detected in the F_6:8 than the F_2:3 generation. Totalled over all five traits, 41 (B91) to 69% (B73) of the QTLs for tester effects and 67% of the QTLs for MTC detected in the F_2:3 generation were verified in the F_6:8 generation. Although differences in relative rank of the QTL effects across generations were observed, especially for the flowering traits, parental contributions were nearly always consistent. Several (8–11) QTLs were identified with effects for all three tester populations and for all traits except the anthesis-silk interval, which had only two such regions. Over all five traits, previous evaluations in this population identified 26 QTLs with consistent effects for two (F_2:3, F_6:8) inbred-progeny evaluations, and 20 (77%) were also associated with MTC in at least one of the generations evaluated herein. In all instances of common inbred and TC QTLs, parental contributions were the same. Received: 26 November 1999 / Accepted: 18 April 2000     

Plasmodium vivax Diversity and Population Structure across Four Continents

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (F _ST>0.2). Outside Central Asia F _ST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.     

Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, II

Population samples including mother-offspring combinations provide information on the selection components: zygotic selection, sexual selection, gametic seletion and fecundity selection, on the mating pattern, and on the deviation from linkage equilibrium among the loci studied. The theory for the analysis of a sample consisting of adult individuals including combinations of a mother and one randomly chosen offspring in the case of n polymorphic autosomal loci with m_a alleles at the ath locus, a = 1, 2,…, n, is developed for an organism with discrete non-overlapping generations. In this general analysis complete determination of the genotypes is assumed. The modifications in the analysis for the case n = 2 and m₁ = m₂ = 2 when the two double heterozygotes cannot be separated are discussed, and the analysis is illustrated by data from a population of Zoarces viviparus (a marine teleost).     

Genetic studies of corn (Zea mays L.) anther culture response

Summary Anthers of two maize (Zea mays L.) inbred lines, DBTS (P₁) and B73 (P₂), their F₁, F₂ and first backcross generations — F₁ x DBTS (B₁), and F₁ x B73 (B₂) — were float cultured in YP medium to study the inheritance of corn anther culturability using generation mean analysis. Significant effects of generation were observed for the three traits measured: anther response (%), frequency of embryos (%) and anther productivity. Variation among the generations was similar for anther response and frequency of embryos: no significant differences were found among the P₁, F₁, F₂ and B₁ means, but the means of P₂ and B₂ were significantly lower than those of the other generations. For anther productivity, the F₂ generation tended to have a slightly higher tendency for multiple embryo formation. A simple additive-dominance model was adequate in explaining the inheritance of anther response and frequency of embryos, but digenic epistasis (additive x dominance) was involved in the inheritance of anther productivity. Additive genetic variance was higher than non-additive genetic variance for all the traits; however, only environmental variance was significant. Narrow-sense heritability estimates were 65% and 75% for anther response and frequency of embryos, respectively. Significant inter-plant variation was observed within generations, even for the inbred line DBTS, but isozymic analysis involving five enzyme loci did not reveal any genotypic variability within the inbred lines DBTS and B73.     

Identification of quantitative trait loci controlling resistance to gray leaf spot disease in maize

Breeding maize for gray leaf spot (GLS) resistance has been hindered by the quantitative nature of the inheritance of GLS resistance and by the limitations of selection under less than optimumal disease pressure. In order to identify the quantitative trait loci (QTLs) controlling GLS resistance, a cross was made between B73 (susceptible) and Va14 (resistant) to generate a large F₂ population. Six GLS disease assessments were made throughout the disease season for over 1000 F₂ plants in 1989, and for 600 F₂-derived F₃ lines replicated in two blocks in 1990. RFLP analysis for78 marker loci representing all ten maize chromosomes was conducted in 239 F₂ individuals including those with the extreme GLS disease phenotypes. The GLS disease scores of the three field evaluations, each averaged over six ratings, were separately used for the interval mapping in order to determine the consistency of the QTL effects. The heavy GLS disease pressure, meticulous disease ratings, and large population size of this study afforded us the sensitivity for detecting QTL effects. QTLs located on three chromosomes (1, 4, and 8) had large effects on GLS resistance, each explaining 35.0–56.0%, 8.8–14.3%, and 7.7–11.0% of the variance, respectively. These three QTL effects were remarkably consistent across three disease evaluations over 2 years and two generations. Smaller QTL effects were also found on chromosomes 2 and 5, but the chromosome-5 effect might be a false positive because it was not repeatable even in the same location. The chromosome-1 QTLs had the largest effect or highest R² reported for any quantitative trait to-date. Except for the chromosome-4 gene, which was from the susceptible parent B73, the resistance alleles at all QTL were derived from Va14. The resistance QTLs on chromosomes 1 and 2 appear to have additive effects, but those on chromosomes 4 and 8 are dominant and recessive, respectively. Significant interaction between the QTLs on chromosomes 1 and 4 was detected in all three evaluations. Cumulatively, the four QTLs identified in this study explained 44, 60, and 68% of the variance in F₂, and in F₃ replications 1 and 2, respectively.     

Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna,Sicily

Studies of hybridizing species can reveal much about the genetic basis and maintenance of species divergence in the face of gene flow. Here we report a genetic segregation and linkage analysis conducted on F₂ progeny of a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius that form a hybrid zone on Mount Etna, Sicily, aimed at determining the genetic basis of intrinsic hybrid barriers between them. Significant transmission ratio distortion (TRD) was detected at 34 (∼27%) of 127 marker loci located in nine distinct clusters across seven of the ten linkage groups detected, indicating genomic incompatibility between the species. TRD at these loci could not be attributed entirely to post-zygotic selective loss of F₂ individuals that failed to germinate or flower (16.7%). At four loci tests indicated that pre-zygotic events, such as meiotic drive in F₁ parents or gametophytic selection, contributed to TRD. Additional tests revealed that cytonuclear incompatibility contributed to TRD at five loci, Bateson–Dobzhansky–Muller (BDM) incompatibilities involving epistatic interactions between loci contributed to TRD at four loci, and underdominance (heterozygote disadvantage) was a possible cause of TRD at one locus. Major chromosomal rearrangements were probably not a cause of interspecific incompatibility at the scale that could be examined with current map marker density. Intrinsic genomic incompatibility between S. aethnensis and S. chrysanthemifolius revealed by TRD across multiple genomic regions in early-generation hybrids is likely to impact the genetic structure of the natural hybrid zone on Mount Etna by limiting introgression and promoting divergence across the genome.     

Quantifying realized inbreeding in wild and captive animal populations

Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression—namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient F_Ped obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (F_Ped=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.     

Population Genetic Structuring in Opisthorchis viverrini over Various Spatial Scales in Thailand and Lao PDR

Khon Kaen Province in northeast Thailand is known as a hot spot for opisthorchiasis in Southeast Asia. Preliminary allozyme and mitochondrial DNA haplotype data from within one endemic district in this Province (Ban Phai), indicated substantial genetic variability within Opisthorchis viverrini. Here, we used microsatellite DNA analyses to examine the genetic diversity and population structure of O. viverrini from four geographically close localities in Khon Kaen Province. Genotyping based on 12 microsatellite loci yielded a mean number of alleles per locus that ranged from 2.83 to 3.7 with an expected heterozygosity in Hardy–Weinberg equilibrium of 0.44–0.56. Assessment of population structure by pairwise F_ST analysis showed inter-population differentiation (P<0.05) which indicates population substructuring between these localities. Unique alleles were found in three of four localities with the highest number observed per locality being three. Our results highlight the existence of genetic diversity and population substructuring in O. viverrini over a small spatial scale which is similar to that found at a larger scale. This provides the basis for the investigation of the role of parasite genetic diversity and differentiation in transmission dynamics and control of O. viverrini.     

Genetic Diversity in Introduced Golden Mussel Populations Corresponds to Vector Activity

We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic structure across native and introduced regions. Introduced populations in Asia exhibit higher genetic diversity (H _E = 0.667–0.746) than those in South America (H _E = 0.519–0.575), suggesting higher introduction effort for the former populations. We observed pronounced geographical structuring in introduced regions, as indicated by both mitochondrial and nuclear markers based on multiple genetic analyses including pairwise Ф_ST, F _ST, Bayesian clustering method, and three-dimensional factorial correspondence analyses. Pairwise F _ST values within both Asia (F _ST = 0.017–0.126, P = 0.000–0.009) and South America (F _ST = 0.004–0.107, P = 0.000–0.721) were lower than those between continents (F _ST = 0.180–0.319, P = 0.000). Fine-scale genetic structuring was also apparent among introduced populations in both Asia and South America, suggesting either multiple introductions of distinct propagules or strong post-introduction selection and demographic stochasticity. Higher genetic diversity in Asia as compared to South America is likely due to more frequent propagule transfers associated with higher shipping activities between source and donor regions within Asia. This study suggests that the intensity of human-mediated introduction vectors influences patterns of genetic diversity in non-indigenous species.     

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N=274). These SNPs were variable both in wild (H_E=0.107) and domestic cats (H_E=0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise F_CT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average F_CT>0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS'' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest F_CT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.     

QTL mapping for fiber quality traits across multiple generations and environments in upland cotton

Identification of quantitative trait loci (QTL) for fiber quality traits that are stable across multiple generations and environments could facilitate marker-assisted selection for improving cotton strains. In the present study, F₂, F_2:3, and recombinant inbred lines (RILs, F _6:8 ) populations derived from an upland cotton (Gossypium hirsutum L.) cross between strain 0-153, which has excellent fiber quality, and strain sGK9708, a commercial transgenic cultivar, were constructed for QTL tagging of fiber quality. We used 5,742 simple sequence repeat primer pairs to screen for polymorphisms between the two parent strains. Linkage maps of F₂ and RILs were constructed, containing 155 and 190 loci and with a total map distance of 959.4 centimorgans (cM) and 700.9?cM, respectively. We screened fiber quality QTL across multiple generations and environments through composite interval mapping of fiber quality data. Specifically, we studied F₂ and F_2:3 family lines from Anyang (Henan Province) in 2003 and 2004 and RILs in Anyang in 2007 and Anyang, Quzhou (Hebei Province), and Linqing (Shandong Province) in 2008. We identified 50 QTL for fiber quality: 10 for fiber strength, 10 for fiber length, 10 for micronaire, eight for fiber uniformity, and 12 for fiber elongation. Nine of these fiber quality QTL were identified in F₂, F_2:3 and RILs simultaneously. Two QTL for fiber strength on chromosomes C7 and C25 were detected in all three generations and all four environments and explained 16.67?C27.86% and 9.43?C21.36% of the phenotypic variation, respectively. These stable QTL for fiber quality traits could be used for marker assisted selection.     

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

Inbreeding (mating between relatives) can dramatically reduce the fitness of offspring by causing parts of the genome to be identical by descent. Thus, measuring individual inbreeding is crucial for ecology, evolution and conservation biology. We used computer simulations to test whether the realized proportion of the genome that is identical by descent (IBD_G) is predicted better by the pedigree inbreeding coefficient (F_P) or by genomic (marker-based) measures of inbreeding. Genomic estimators of IBD_G included the increase in individual homozygosity relative to mean Hardy–Weinberg expected homozygosity (F_H), and two measures (F_ROH and F_E) that use mapped genetic markers to estimate IBD_G. IBD_G was more strongly correlated with F_H, F_E and F_ROH than with F_P across a broad range of simulated scenarios when thousands of SNPs were used. For example, IBD_G was more strongly correlated with F_ROH, F_H and F_E (estimated with ⩾10 000 SNPs) than with F_P (estimated with 20 generations of complete pedigree) in populations with a recent reduction in the effective populations size (from N_e=500 to N_e=75). F_ROH, F_H and F_E generally explained >90% of the variance in IBD_G (among individuals) when 35 K or more SNPs were used. F_P explained <80% of the variation in IBD_G on average in all simulated scenarios, even when pedigrees included 20 generations. Our results demonstrate that IBD_G can be more precisely estimated with large numbers of genetic markers than with pedigrees. We encourage researchers to adopt genomic marker-based measures of IBD_G as thousands of loci can now be genotyped in any species.