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PubMed2004

Effect of pubescence tip on soybean resistance to lepidopteran insects.

DNA marker analysis has mapped a quantitative trait locus for soybean, Glycine max (L.) Merr., resistance to the corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), on the USDA soybean genetic linkage map near the classical gene Pb, which conditions pubescence tip. This study was initiated to determine the effect of pubescence tip on resistance to H. zea larvae and to examine the effect on beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), and soybean looper, Pseudoplusia includens (Walker) (Lepidoptera: Noctuidae), larvae. The effect of blunt (pb) and sharp (Pb) pubescence tip was tested in antixenosis and antibiosis bioassays on H. zea, S. exigua, and P. includens larvae with near-isolines and insect-resistant and -susceptible genotypes differing in pubescence tip morphology. Sharp pubescence tip significantly reduced defoliation (antixenosis) from H. zea, S. exigua, and P. includens and weight gain (antibiosis) of H. zea. The weight gain of P. includens was unaffected, and S. exigua weight gain was significant for one pair of near-isolines differing in pubescence tip but not the other. The results indicate that sharp pubescence tip would be beneficial to introgress into elite soybean germplasm due to its association with resistance to H. zea, S. exigua, and P. includens.

Animals↗

PubMed2000

Annuality, perenniality and cell death.

This essay considers annuality and perenniality as quantitative traits and discusses the application of established and new genetic tools to the analysis of plant life histories. Annual/perennial status is a function of meristem determinacy in combination with the processes of cell death and disposal employed by plants to generate well-adapted anatomies and morphologies. Creeping perennials, like clover or bracken, seem to move around in the environment. They do this by extending into unoccupied space while the oldest tissues behind the growing and mature regions senesce, die and decompose. Trees do essentially the same thing, except that they develop vertically and the old dead tissue does not disappear but instead persists as wood. A root system is a kind of upended vertical perennial. The balance between exploratory growth and the wave of tissue death that succeeds it is a major determinant of perenniality. So although perenniality and annuality may appear to be dramatically different traits, extremes of behaviour can arise by a relatively minor change in the relationship between growth and death. This conclusion is supported by evidence from genome dosage studies, from the practical experiences of breeding perennial-type traits into annual backgrounds and from molecular cladistics. Applications of methods for the genetic analysis of quantitative characters are described, including the exploitation of introgression mapping in Lolium-Festuca and quantitative trait locus mapping in cereals and other species.

Apoptosis↗

PubMedDate not supplied

Founder effects and the genetic structure of Coulter pine.

Mean expected heterozygosity at 33 isozyme loci decreased with latitude from 0.193 near the southern extreme of Coulter pine's range to 0.107 at its northern extreme. This decrease was paralleled by a loss of alleles north of the Peninsular Ranges of southern California. Fifteen alleles dropped out along the roughly lineal range, at points coincident with large gaps in the species' distribution. The pattern may reflect a cascading series of founder events as Coulter pine invaded the Trans. verse Ranges and the South Coast Ranges from Pleistocene refugia. Alleles were not replaced following colonization, probably because migration, Nm, among populations is only 0.74-1.27, depending on estimator, the lowest values reported in any pines. Wright's (F(ST)) indicated that 16.5% of the total genic diversity is among populations. The fixation index, (F(IS)) of 0.072 indicated only a moderate excess of homozygotes. However, the northernmost outlier had significant excess homozygosity (F = 0.253). Hybridization may also play a role in the genetic structure of Coulter pine: 16 alleles were novel, or private, occurring only where Coulter pine was sympatric with Jeffrey pine, particularly at San Benito Mountain. Some of these novel alleles could be the result of introgression from Jeffrey pine, or possibly represent hybrizymes, products of intragenic recombination between genomes.

Alleles↗

PubMedDate not supplied

A recessive allele inhibiting saponin synthesis in two lines of Bolivian quinoa (Chenopodium quinoa Willd.).

Quinoa cultivars currently grown in North America and Europe require removal of bitter-tasting saponins from the grain prior to human consumption. This need for postharvest processing is a barrier to expanding production of the crop outside its Andean area of origin. Grain saponin content in quinoa shows continuous variation and is considered to be a quantitative trait. However, segregation for the presence or absence of grain saponin in F2 generations derived from crosses between high- and low-saponin parents indicates a major gene effect, with plants homozygous for a recessive allele spl having no detectable grain saponin. Variation in saponin levels among F2 plants with detectable grain saponin was consistent with polygenic inheritance. It appears that grain saponin level in quinoa is both qualitatively and quantitatively controlled, with saponin production requiring at least one dominant allele at the Sp locus and the amount of grain saponin being determined by an unknown number of additional quantitative loci. Introgression of sp1 into day-neutral lines will facilitate the development of short-season "sweet" quinoa cultivars which do not require postharvest processing to remove grain saponin.

Alleles↗

PubMedDate not supplied

Maize tertiary trisomic stocks derived from B-A translocations.

Reciprocal translocations between supernumerary B chromosomes and the basic complement of A chromosomes in maize have resulted in a powerful set of tools to manipulate the dosage of chromosomal segments. From 15 B-A reciprocal translocation stocks that have the B-A chromosome genetically marked we have developed tertiary trisomic stocks. Tertiary trisomics are 2n + 1 aneuploids where the extra chromosome is a translocation element, in this case a B-A chromosome. Whereas B-A translocations produce aneuploidy in the sperm, the tertiary trisomic plant efficiently transmits hyperploid gametes maternally. Because the B-A tertiary trisomic stocks and the B-A translocation stocks from which they were derived are introgressed into the W22 inbred line, the effects of maternally and paternally transmitted trisomic B-A chromosomes can be compared. Data are presented on both the male and female transmission rates of the B-A chromosomes in the tertiary trisomic stocks.

Chromosomes, Plant↗

PubMedDate not supplied

A partial african ancestry for the creole cattle populations of the Caribbean.

Seventy-eight cattle samples from three Creole Caribbean islands and one Brazilian breed were analyzed for sequence variation in the hypervariable segment of the mitochondrial DNA control region. Seventy-three samples displayed Bos taurus haplotypes, and five samples exhibited haplotypes that were of Bos indicus ancestry. Phylogenetic analysis revealed that all sampled B. taurus sequences fell into two distinct clusters with separate African and European origins. European sequences were encountered in each population; however, the distribution of African haplotypes was uneven, with the highest proportion of African influence found in the Guadeloupe Creole. The reduced levels of African haplotypic variation within the Caribbean and Brazilian are consistent with prior founder effects. Additionally, genetic variation at three microsatellite loci illustrated African influence uniquely in the Guadeloupe Creole. Collectively, the data suggest that this African influence is, at least in part, attributable to the historical importation of African cattle to the Americas. Furthermore, alleles of B. indicus ancestry were detected at appreciable frequencies in all Caribbean Creole populations and may reflect zebu introgressions from either West Africa or the Indian subcontinent.

Africa↗

PubMedDate not supplied

Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex.

The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close to each other in all three species. An evolutionary tree based on the variation at these three loci revealed that the populations from the different species are completely intermixed in the tree. This was supported by hierarchical F-statistics where the between-species component was zero. At a fourth locus, Gpi (glucose phosphate isomerase), the species differ substantially. This locus is sex linked in J. ischiosetosa, but in the two other species, J. albifrons and J. praehirsuta, it is either found on autosomes or is sex linked with a high recombination rate between the locus and the centromere. An evolutionary tree for this locus partitions the populations into separate groups and a hierarchical F-statistic has a between-species component of about 50%. The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes.

Animals↗

PubMed2026

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗

PubMed2026

The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

asexuality↗

PubMedDate not supplied

Predominant African-derived mtDNA in Caribbean and Brazilian Creole cattle is also found in Spanish cattle (Bos taurus).

African-derived mitochondrial DNA (mtDNA) have been described in South American and Caribbean native cattle populations, which could have been introduced into America from Iberia or by direct importation from Africa. However, the similarity among described haplotypes is not known. We examined mtDNA variation in Guadeloupe Creole and Spanish cattle in an attempt to identify African-derived mtDNA haplotypes and compare them with those previously described. Eleven haplotypes clustered into the European taurine haplogroup (T3), two haplotypes into the African taurine (T1) haplogroup, and three haplotypes into the African-derived American haplogroup (AA). The AA1 and Eucons haplotypes were the most frequently observed. The presence of the AA haplogroup in Spanish cattle confirms historical records and genetic evidence of Iberian cattle as the main source of American native cattle origin. The possible origin of African-derived mitochondrial haplotypes in Iberian and Creole cattle is discussed, and the accumulated evidence does not support a founder effect from African ancestral cattle by direct importations. The presence of taurine AA and T3 haplotypes in Brazilian Nellore may indicate introgression by local European-derived cattle. Data presented in this work will contribute to the understanding of the origin of Guadeloupe Creole cattle.

Africa↗

PubMed2005

Simple sequence repeat marker associated with a natural leaf defoliation trait in tetraploid cotton.

Cotton (Gossypium hirsutum L.) leaf defoliation has a significant ecological and economical impact on cotton production. Thus the utilization of a natural leaf defoliation trait, which exists in wild diploid cotton species, in the development of tetraploid cultivated cotton will not only be cost effective, but will also facilitate production of very high-grade fiber. The primary goal of our research was to tag loci associated with natural leaf defoliation using microsatellite markers in Upland cotton. The F2 populations developed from reciprocal crosses between the two parental cotton lines--AN-Boyovut-2 (2n = 52), a late leaf defoliating type, and Listopad Beliy (2n = 52), a naturally early leaf defoliating type--demonstrated that the naturally early leaf defoliation trait has heritability values of 0.74 and 0.84 in the reciprocal F2 population. The observed phenotypic segregation difference in reciprocal crosses suggested a minor cytoplasmic effect in the phenotypic expression of the naturally early leaf defoliation trait. Results from the Kruskal-Wallis (KW) nonparametric test revealed that JESPR-13 (KW = 6.17), JESPR-153 (KW = 9.97), and JESPR-178 (KW = 13.45) Simple sequence repeat (SSR) markers are significantly associated with natural leaf defoliation in the mapping population having stable estimates at empirically obtained critical thresholds (P < .05-.0001). JESPR-178 revealed the highest estimates (P < .0001) for association with the natural leaf defoliation trait, exceeding maximum empirical threshold values. JESPR-178 was assigned to the short arm of chromosome 18, suggesting indirectly that genes associated with natural leaf defoliation might be located on this chromosome. This microsatellite marker may have the potential for use to introgress the naturally early leaf defoliation quantitative trait loci (QTL) from the donor line Listopad Beliy to commercial varieties of cotton through marker-assisted selection programs.

Chromosomes, Plant↗

PubMed2005

Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe.

Sequence variation present within the mitochondrial genome was used to investigate genetic diversity within sheep breeds from Asia and Europe. Comparison of 2027 bp of sequence from 121 animals revealed 44 phylogenetically informative nucleotide positions and a single insertion/deletion. A total of 57 haplotypes were observed which formed two distinct clades. Type A haplotypes were found in breeds from Asia (India, Indonesia, Mongolia, and Tibet), while type B haplotypes were observed at the highest frequency in breeds sourced from Europe (nine breeds from Austria, Aland, Finland, Spain, and northwestern Russia). The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date. Only 2.7% of the sequence variation observed was partitioned between continents, which is lower than both goat (approximately 10%) and cattle (approximately 50%). Diagnostic restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) tests which distinguish type A and B haplotypes were used to test an additional 223 animals from 17 breeds of European and Asian origin. A mixture of the two lineages was found in every breed except Suffolk and the Indian Garole, indicating introgression has played a major part during breed development and subsequent selection.

Animals↗

PubMed2005

The origins of Iberian horses assessed via mitochondrial DNA.

Despite a number of recent studies that have focused on the origin of domestic horses, genetic relationships between major geographical clusters still remain poorly understood. In this study we analyzed a 296 bp mtDNA fragment from the HVI region of 171 horses representing 11 native Iberian, Barb, and Exmoor breeds to assess the maternal phylogeography of Iberian horses. The mtDNA haplogroup with a CCG motif (nucleotide position 15,494 to 15,496) was the most frequent in Iberian and Barb breeds (0.42 and 0.57, respectively), regardless of geographic location or group of breeds. This finding supports the close genetic relationship between the ancestral mare populations of the Iberian Peninsula and Northern Africa. Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Our results also suggest that Northern Iberian ponies--which are phenotypically close to British ponies, especially Exmoor--are the result of an introgression rather than population replacement.

Animals↗

PubMed2006

Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.).

Although sunflower was long thought to be the product of a single domestication in what is now the east-central United States, recent archaeological and genetic evidence have suggested the possibility of an independent origin of domestication, perhaps in Mexico. We therefore used hypervariable chloroplast simple-sequence repeat markers to search for evidence of a possible Mexican origin of domestication. This work resulted in the identification of 45 chloroplast haplotypes from 26 populations across the range of wild sunflower as well as 3 haplotypes from 15 domesticated lines, representing both primitive and improved cultivars. The 3 domesticated haplotypes were characterized by 1 primary haplotype (found at a frequency of 6.7% in the wild) as well as 2 rare haplotypes, which are most likely the products of mutation or introgression. One of these rare haplotypes was not observed in the wild, bringing the total number of haplotypes identified to 46. A principal coordinate analysis revealed the presence of 3 major haplotype clusters, one of which contained the primary domesticated haplotype, the 2 rare domesticated variants, as well as haplotypes found across much of the range of wild sunflower. The Mexican haplotypes, on the other hand, fell well outside of this cluster. Although our data do not provide insight into the specific location of sunflower domestication, the relative rarity of the primary domesticated haplotype in the wild, combined with the dissimilarity between this haplotype and those found in the Mexican populations surveyed, provides further evidence that the extant domesticated sunflowers are the product of a single domestication event somewhere outside of Mexico.

Cluster Analysis↗

PubMed2006

Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites.

In the present report, the polymorphisms from 9 microsatellites were used to assess genetic diversity and relationships in 4 Creole cattle breeds from Argentina and Bolivia, 4 European taurine breeds, and 2 American zebu populations. The Creole populations display a relatively high level of genetic variation as estimated by allelic diversity and heterozygosity, whereas the British breeds displayed reduced levels of genetic diversity. The analysis of molecular variance indicated that 7.8% of variance can be explained by differences among taurine and zebu breeds. Consistent with these results, the first principal component (PC), which comprised the 40% of the total variance, clearly distinguishes these 2 groups. In addition, all constructed phylogenetic trees cluster together Nelore and Brahman breeds with robust bootstrap values. Only 1% of variance was due to difference between American Creole and European taurine cattle. Although this secondary split was supported by the classical genetic distance and the second PC (15%), the topology of trees is not particularly robust. The presence of zebu-specific alleles in Creole cattle allowed estimating a moderate degree of zebu admixture. When these data were compared with mitochondrial and Y chromosomal studies, a clear pattern of male-mediated introgression was revealed. The results presented here contribute to the understanding of origin and history of the American Creole cattle.

Alleles↗

PubMed2006

Pennisetum squamulatum: is the predominant cytotype hexaploid or octaploid?

Apomixis is a mode of asexual reproduction where maternal clones are produced through seeds. Consequently, genetic segregation is prevented in hybrid progenies. Pennisetum squamulatum has been used to transfer apomixis into the related sexual species Pennisetum glaucum by the introgression of an apospory-specific genomic region (ASGR)-carrier chromosome. Crosses between P. glaucum and P. squamulatum or Pennisetum purpureum have been relatively easy to make even though P. squamulatum has been reported to have a different basic chromosome number than the other 2 species (9 vs. 7) and to be hexaploid (2n = 6x = 54). Our extensive examination of one accession had shown a chromosome number of 2n = 56. In order to determine if there was a variation among accessions, we counted the number of chromosomes in 5 accessions of P. squamulatum using centromeric and 18S-5.8S-26S rDNA probes as molecular cytological markers. Our results showed that P. squamulatum is most likely octaploid with a basic chromosome number of 7 (2n = 8x = 56) and may belong to the secondary gene pool of Pennisetum. Moreover, a morphologically similar ASGR-carrier chromosome that confers apomixis was observed in all accessions.

Chromosomes, Artificial, Bacterial↗

PubMed2006

Mitochondrial DNA sequence variation in Portuguese native dog breeds: diversity and phylogenetic affinities.

In an extensive survey of the genetic diversity in Portuguese dogs, we have examined an 887-bp fragment of the mitochondrial DNA (mtDNA) from 8 Portuguese, 1 Spanish, and 2 North African native dog breeds, including village dogs from Portugal and Tunisia. Forty-nine haplotypes were found in the 164 individuals analyzed, with private haplotypes being found in several breeds. For example, the Castro Laboreiro Watchdog, a rare breed from a small and isolated region in Portugal, was monomorphic for mtDNA and possessed a new haplotype, which may be provisionally considered a breed-specific marker. Phylogenetic analyses recapitulated 4 major clades identified in other studies, but new haplotypes, grouping within a clade that was previously thought as geographically restricted, were detected in Portugal and Morocco. Portuguese village dogs showed no genetic differentiation from nonnative dogs or from local breeds of the areas in which the village dogs were sampled. Although Iberian and North African dog breeds possessed breed-specific mtDNA haplotypes, no significant geographic structure could be detected among them. There is no evidence for introgression of North African haplotypes in Iberian dogs, contrary to previous results for other domestic animals.

Animals↗

PubMed2007

Searching the genomes of inbred mouse strains for incompatibilities that reproductively isolate their wild relatives.

Identification of the genes that underlie reproductive isolation provides important insights into the process of speciation. According to the Dobzhansky-Muller model, these genes suffer disrupted interactions in hybrids due to independent divergence in separate populations. In hybrid populations, natural selection acts to remove the deleterious heterospecific combinations that cause these functional disruptions. When selection is strong, this process can maintain multilocus associations, primarily between conspecific alleles, providing a signature that can be used to locate incompatibilities. We applied this logic to populations of house mice that were formed by hybridization involving two species that show partial reproductive isolation, Mus domesticus and Mus musculus. Using molecular markers likely to be informative about species ancestry, we scanned the genomes of 1) classical inbred strains and 2) recombinant inbred lines for pairs of loci that showed extreme linkage disequilibria. By using the same set of markers, we identified a list of locus pairs that displayed similar patterns in both scans. These genomic regions may contain genes that contribute to reproductive isolation between M. domesticus and M. musculus. This hypothesis can now be tested using laboratory crosses and surveys of introgression in the wild.

Animals↗