Ancestral Lines Research Articles

Foliar resistance to ozone injury in the genetic base of U.S. and Canadian soybean and prediction of resistance in descendent cultivars using coefficient of parentage

Development of ozone (O 3)-resistant cultivars is a potentially important approach for maintaining crop productivity under future climate scenarios in which tropospheric O 3 pollution is projected to rise. A first step in the breeding of resistant cultivars for a crop such as soybean ( Glycine max (L.) Merr.) is identification of sources of O 3 resistance genes. Thirty ancestral lines of soybean were screened for differences in O 3 foliar injury under greenhouse conditions. The ancestors represented 92% of the genetic base of North American soybean as determined by pedigree analysis. Injury among ancestors ranged from 5 to 50% of leaf area, based on response of the five oldest main stem leaves, indicating both the presence of substantial genetic variation for O 3 injury among the ancestors as well as resistance levels greater than that of the standard control cultivar, resistant Essex (15% injury). Ancestral types Fiskeby 840-7-3 and Fiskeby III exhibited the greatest foliar resistance and PI 88788 the least. A subsequent field study confirmed the foliar resistance of the Fiskeby types. Resistant ancestors identified here are proposed for inheritance and DNA mapping studies to determine the genetic basis of foliar resistance. Because the presence of O 3-resistant ancestors suggested that resistant descendents may exist in addition to the resistant control Essex, a method was developed to facilitate their identification. A predicted O 3-resistance score was calculated for 247 publicly-released cultivars, based on pedigree analysis and ancestral response to ozone. Using this approach, the 32 public cultivars most closely related to resistant ancestors and, thus, most likely to be resistant were identified as priority candidates for future screening efforts. Predicted scores from the analysis suggested that cultivars from the Midwest may be more sensitive to foliar injury, on average, than Southern cultivars.

Ancestral matrilineages and mitochondrial DNA diversity of the Lidia cattle breed

To clarify the genetic ancestry and the mitochondrial DNA (mtDNA) diversity of the Lidia cattle breed, a 521-bp D-loop fragment was sequenced in 527 animals belonging to 70 herds distributed across 29 lineages. The mtDNA diversity recorded was similar to that seen for Middle Eastern breeds and greater than that recorded for the majority of European breeds. Haplotype T3 was the most common (81%), followed by the African T1 haplotype (17%); very low frequencies were recorded for haplotypes T and T2. The results agree with there being two major ancestral lines for the Lidia breed, European and African, similar to that seen for other Mediterranean breeds. A wide range of variation in haplotype frequencies was seen between the examined lineages. Haplotype T3 was present in all those analysed; in five it was the only one present, and in only one lineage (Miura) was its frequency lower than that of T1. T1*, a haplotype reported in Criollo breeds and to date in only a single European breed (the Retinta breed from Spain), was found in a single animal belonging to the Concha y Sierra lineage. Network analysis of the Lidia breed revealed the presence of two major haplotypes: T3 and T1. The Lidia breed appears to be more closely related to prehistoric Iberian and Italian than to British aurochs.

Identification of Soybean Accessions with High Germinability in High‐Temperature Environments

Soybean [Glycine max (L.) Merr.] seed produced in high‐temperature, high‐humidity production environments is prone to have substandard germination. Hardseededness, wrinkled seed coats, and infection by Phomopsis longicolla Hobbs are all known to affect soybean seed germinability. Ancestors of modern U.S. soybean cultivars may lack the necessary variability to impart high germinability to new cultivars without the introgression of new genetic diversity. The purpose of this research was to identify soybean germplasm possessing positive traits affecting high seed germinability for seed produced under high‐temperature environments, such as in the early soybean production system (ESPS) of the midsouthern United States. Seed was produced in the ESPS for 486 U.S. plant introductions (PI), 25 ancestral lines of U.S. cultivars, and four U.S. cultivars at Stoneville, MS, in 2002 and 2003. Standard and accelerated‐aging germination percentages, hardseededness, seed coat wrinkling, and incidence of P. longicolla were estimated for each line. Based on the 2002 and 2003 field data, 42 PIs were selected for further testing, along with three cultivars, in two greenhouse temperature regimes (36° and 42°C) at Stoneville, MS, in 2005. Standard field germinations for the 25 ancestral lines ranged from 26 to 82%. Sixty‐three accessions were identified as having a mean standard field germination of ≥90%, <10% hard seed and P. longicolla infection, and ≤10% wrinkled seed coat. Genotypes with excellent seed traits have now been identified for soybean breeders to use in developing improved cultivars with high seed germinability for use in high‐temperature production environments.

Ancestral lines: the Maisin of Papua New Guinea and the fate of the rainforest

More than a century of interaction with colonial and global agencies and forces have brought many changes to the lives of the Maisin people who live on the northeastern coast of Papua New Guinea. Yet ancestral traditions continue to strongly inform their way of life. Their beautifully designed tapa cloth, made from the pounded inner bark of the paper mulberry tree, most vividly connects the past with the present. Using the various stages of tapa cloth production to frame a broader discussion of changes and continuities in Maisin culture (economic pursuit, social arrangements, gender relations, religion, politics, and the environment) Barker offers a nuanced understanding of how the Maisin came to reject commercial logging on their traditional lands. Viewed in isolation, the decision appears to be a confirmation of tradition over modernity. Yet the book shows that it is the most recent, and perhaps dramatic, instance in a long chain of improvisations and compromises that have allowed the Maisin to remain true to core ancestral values while participating in wider social, political, and economic systems. Ancestral Lines provides an important counterpoint to the stereotype of indigenous peoples as passive victims of impersonal global forces. While accessible to most readers, including those with little or no knowledge of Melanesia or anthropology, Ancestral Lines has been designed with introductory anthropology courses in mind. Each chapter opens with a description of succeeding stages in the creation and use of a piece of tapa cloth. These, in turn, lead into discussions of dimensions of Maisin life that correspond to the sections and order of most standard introductory textbooks.

Simulating the evolution of a clonal trait in plants with sexual and vegetative reproduction

Aims Phenotypic optimality models neglect genetics. However, especially when heterozygous genotypes are fittest, evolving allele, genotype and phenotype frequencies may not correspond to predicted optima. This was not previously addressed for organisms with complex life histories. Methods Therefore, we modelled the evolution of a fitness-relevant trait of clonal plants, stolon internode length. We explored the likely case of an asymmetric unimodal fitness profile with three model types. In constant selection models (CSMs), which are gametic, but not spatially explicit, evolving allele frequencies in the one-locus and fiveloci cases did not correspond to optimum stolon internode length predicted by the spatially explicit, but not gametic, phenotypic model. This deviation was due to the asymmetry of the fitness profile. Gametic, spatially explicit individual-based (SEIB) modeling allowed us relaxing the CSM assumptions of constant selection with exclusively sexual reproduction. Important findings For entirely vegetative or sexual reproduction, predictions of the gametic SEIB model were close to the ones of spatially explicit nongametic phenotypic models, but for mixed modes of reproduction they approximated those of gametic, not spatially explicit CSMs. Thus, in contrast to gametic SEIB models, phenotypic models and, especially for few loci, also CSMs can be very misleading. We conclude that the evolution of traits governed by few quantitative trait loci appears hardly predictable by simple models, that genetic algorithms aiming at technical optimization may actually miss the optimum and that selection may lead to loci with smaller effects in derived compared with ancestral lines.

The Effect of Tropical Sorghum Conversion and Inbred Development on Genome Diversity as Revealed by High‐Resolution Genotyping

Graphical genotypes have been generated for a set of sorghum [Sorghum bicolor (L.) Moench] germplasm, which includes selected public inbreds, germplasm from the world collection, and ancestral lines central to the early breeding efforts of sorghum. We have focused our present examination on sorghum chromosome SBI‐06, which encodes ma1 and dw2, two genes critical to sorghum improvement dating to the original introduction of tropical sorghums into the United States. Utilizing the pedigree relationship between sorghum cultivars, the patterns of genetic variation were detailed within segmental chromosomal blocks of SBI‐06. Segmental genomic blocks were traced back through multiple generations of a pedigree, often back to founder tropical accessions. The graphical genotypes reveal genomic signatures of historical breeding decisions, especially evidence of directional selection during the conversion of tropical accessions to temperate adaptation. This information is central to our efforts to understand those crop improvement processes that have shaped the genomic diversity of elite sorghum cultivars.

Evaluation of Genetic Diversity and Genome‐wide Linkage Disequilibrium among U.S. Wheat ( Triticum aestivum L.) Germplasm Representing Different Market Classes

Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among 43 U.S. wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven U.S. wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the wheat genome. Genetic diversity among these lines was examined using genetic distance-based and model-based clustering methods, and analysis of molecular variance. Four populations were identified from the model-based analysis, which partitioned each of the spring and winter populations into two subpopulations, corresponding largely to major geographic regions of wheat production in the United States. This suggests that the genetic diversity existing among these U.S. wheat germplasm was influenced more by regional adaptation than by market class, and that the individuals clustered in the same model-based population likely shared related ancestral lines in their breeding history. For this germplasm collection, genome-wide LD estimates were generally less than 1 cM for the genetically linked loci pairs. This may result from the population stratification and small sample size that reduced statistical power. Most of the LD regions observed were between loci less than 10 cM apart. However, the distribution of LD was not uniform based on linkage distance and was independent of marker density. Consequently, LD is likely to vary widely among wheat populations. © Crop Science Society of America.

Coalescent lineage distributions

We study identities for the distribution of the number of edges at time t back (i.e. measured backwards) in a coalescent tree whose subtrees have no mutations. This distribution is important in the infinitely-many-alleles model of mutation, where every mutation is unique. The model includes, as a special case, the number of edges in a coalescent tree at time t back when mutation is ignored. The identities take the form of expected values of functions of Zt=eiXt, where Xt is distributed as standard Brownian motion. Associated identities are also found for the distributions of the time to the most recent common ancestor, the time until loss of ancestral lines by coalescence or mutation, and the age of a mutation. Hypergeometric functions play an important role in the identities. The identities are of mathematical interest, as well as potentially being formulae to use for numerical integration or simulation to compute distributions that are usually expressed as alternating-sign series expansions, which are difficult to compute.

Coalescent lineage distributions

We study identities for the distribution of the number of edges at time t back (i.e. measured backwards) in a coalescent tree whose subtrees have no mutations. This distribution is important in the infinitely-many-alleles model of mutation, where every mutation is unique. The model includes, as a special case, the number of edges in a coalescent tree at time t back when mutation is ignored. The identities take the form of expected values of functions of Z t =eiX t , where X t is distributed as standard Brownian motion. Associated identities are also found for the distributions of the time to the most recent common ancestor, the time until loss of ancestral lines by coalescence or mutation, and the age of a mutation. Hypergeometric functions play an important role in the identities. The identities are of mathematical interest, as well as potentially being formulae to use for numerical integration or simulation to compute distributions that are usually expressed as alternating-sign series expansions, which are difficult to compute.

Effect of Six Decades of Selective Breeding on Soybean Protein Composition and Quality: A Biochemical and Molecular Analysis

To evaluate the extent of the genetic change and its effects on the seed protein composition of soybean cultivars released during the past 60 years, representative ancestral cultivars and those derived from selective breeding were grown in a side-by-side comparison. Total seed protein content, determined by combustion analysis of nitrogen, revealed a decline in the protein content after decades of selection and breeding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis comparison of protein profiles of the soybean cultivars indicated that relative expression of most of the seed storage proteins had not varied substantially from the ancestral lines to the present commercial cultivars. There was noticeably less beta-subunit of beta-conglycinin, a protein devoid of sulfur amino acids, in the modern cultivars represented by Mustang, Pioneer 93B09, and Asgrow 3602. Comparison of the amino acid profiles of soybean seed, a benchmark of the protein's nutritional quality, revealed that the ancestral progenitor, G. soja, was significantly higher in cysteine, glutamic acid, histidine, and arginine than either the ancestral or the modern cultivars. Selective breeding over the past 60 years minimally affected the overall amino acid composition. The degree of divergence in the DNA sequence of the genes encoding glycinin and beta-conglycinin in the ancestral and modern cultivars was investigated using Southern hybridization and the polymerase chain reaction. Even though some restriction fragment polymorphisms could be detected, overall, the banding patterns were remarkably similar among the ancestral cultivars and those derived from them, suggesting a high degree of conservation of seed-storage protein genes. The results of our study suggest that selection and breeding for yield during the past 60 years had no major influence on the protein composition, ostensibly because of limited genetic diversity among the parental lines.

Adaptive evolution of secretory cell lines in vertebrate skin

AbstractThe embryonic horny layer of vertebrates contains distinctive cell lines that account for the remarkable, diverse secretory performances of their cutaneous apparatuses. Aquatic classes (jawless, cartilaginous and bony fishes) possess single gland cells, scattered among ordinary epidermal cells, that manufacture proteinaceous or mucous substances. This dichotomy is retained in adult amphibians, although the secretory cells in anamnionic tetrapode begin to be arranged in complex glands located in the loose dermis. In the Amniota, intensive keratinisation involving the epidermis results in the loss of the ancestral secretory lines, accompanied by the onset of a novel, lipid- producing gland type, which in mammals is flanked by the exclusive sweat gland apparatus.In this concise up-to-date review, we attempt to phylogenetically narrow the large variety of secretory structures in vertebrate skin into a few basic schemes, in the light of the close relationships between environmental challenges and ecolo...

A coalescent model for the effect of advantageous mutations on the genealogy of a population

When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample n individuals from a population and trace their ancestral lines backwards in time, many lineages may coalesce almost instantaneously at the time of a selective sweep. We show that as the population size goes to infinity, this process converges to a coalescent process called a coalescent with multiple collisions. A better approximation for finite populations can be obtained using a coalescent with simultaneous multiple collisions. We also show how these coalescent approximations can be used to get insight into how beneficial mutations affect the behavior of statistics that have been used to detect departures from the usual Kingman's coalescent.

Evaluation of Ancestral Lines of U.S. Soybean Cultivars for Resistance to Four Soybean Viruses

Fifty‐two North American (NA) ancestral soybean [Glycine max (L.) Merr.] lines were screened for resistance to Bean pod mottle virus (BPMV), Soybean mosaic virus (SMV) strains G1 and G5, Tobacco ringspot virus (TRSV), and Tobacco streak virus (TSV). Seven ancestors, ‘CNS’, ‘Haberlandt’, ‘Ogden’, ‘Peking’, PI 71506, PI 88788, and ‘Tokyo’, were resistant to SMV‐G1. Sixteen entries, ‘A.K. (Harrow)’, ‘Capital’, CNS, FC 33243, Haberlandt, ‘Illini’, ‘Improved Pelican’, ‘Laredo’, ‘Lincoln’, ‘Mandarin’, ‘Mandarin (Ottawa)’, Ogden, ‘Palmetto’, Peking, PI 88788, and Tokyo were resistant to SMV‐G5. All ancestral lines tested were susceptible to BPMV and TRSV. Only one ancestor, ‘Tanner’, was resistant to TSV. On the basis of cultivar registration articles through 2002, there were 15 public soybean cultivars with reported resistance to SMV. The possible donors of resistance for each were identified. Two soybean ancestors, CNS and Ogden, were the most important possible sources of SMV resistance genes in U.S. commercial soybean cultivars, as the pedigree of 75 and 56% of the reported resistant cultivars contained CNS and Ogden, respectively. In most of the cultivar registration articles, reactions to SMV were not reported. With the relatively high frequency of SMV resistance in major ancestral lines, SMV resistance in U.S. cultivars may be more common than expected.

Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.

Genetic Diversity Among Finnish Six-Rowed Barley Cultivars Based on Cpedigree Information and DNA Markers

Genetic diversity among Finnish six-rowed spring barleys was studied by both pedigree analysis and random amplified polymorphic DNA (RAPD) markers. 26 six-rowed barley varieties have been released by Finnish plant breeders, 22 of which are based on controlled crosses. These 22 varieties originate from 14 ancestors, of which 7 (Olli, Asplund, Vega, Gull, Hanna, Maskin, OAC21) are principal ancestors with a coancestry r 0.05. Contribution of the principal ancestors to the pedigrees of the varieties has not changed significantly during the 60 years of barley breeding in Finland. Jaccard's similarity indices, based on 54 polymorphic RAPD markers, were calculated for a set of modern, ancestral and introgression lines and varieties. Jaccard's indices varied from 0.154 to 0.935, and similarities between related accessions were significantly higher (t-test, P 0.01) than between the unrelated ones. Correlation between kinship coefficients based on pedigrees and Jaccard's indices were weak, and Jaccard's indices varied widely for accessions without a known pedigree. The genetic similarity within the old varieties is comparable to that of the modern varieties.

Putative Alleles for Increased Yield from Soybean Plant Introductions

Improving seed yield of soybean [Glycine max (L.) Merr.] is an important breeding goal. The objective of this study was to evaluate two soybean PIs as sources of alleles for the enhancement of seed yield in North American cultivars. A population of 167 F5–derived lines was developed from a cross between ‘BSR 101’ and the experimental line LG82‐8379. BSR 101 has nine of 10 major ancestral lines contributing to the commercial gene pool of North America, while LG82‐8379 was selected from a cross between PI 68508 and FC 04007B. The F5–derived lines, divided into three sets based on maturity, were evaluated for 145 polymorphic simple sequence repeat (SSR) marker loci and for seed yield and other agronomic traits in 12 environments. Fifteen quantitative trait loci (QTL) were significantly [P < 0.05, likelihood of odds (LOD) > 2.5] associated with seed yield in at least one set with two significant across all sets. For nine of the yield QTL, the LG82‐8379 alleles were associated with yield increases of 1.7 to 5.4% while the BSR 101 alleles increased yield 2.4 to 4.4% at six yield QTL. Four yield QTL were associated with significant changes in R8, eight with plant height, and three with seed protein concentration. Additional QTL were identified for R8, plant height, lodging, and seed protein and oil concentration. These results indicate that soybean PIs have the genetic potential for improving seed yield of U.S. soybean cultivars.

Putative Alleles for Increased Yield from Soybean Plant Introductions

Improving seed yield of soybean [Glycine max (L.) Merr.] is an important breeding goal. The objective of this study was to evaluate two soybean PIs as sources of alleles for the enhancement of seed yield in North American cultivars. A population of 167 F5–derived lines was developed from a cross between ‘BSR 101’ and the experimental line LG82-8379. BSR 101 has nine of 10 major ancestral lines contributing to the commercial gene pool of North America, while LG82-8379 was selected from a cross between PI 68508 and FC 04007B. The F5–derived lines, divided into three sets based on maturity, were evaluated for 145 polymorphic simple sequence repeat (SSR) marker loci and for seed yield and other agronomic traits in 12 environments. Fifteen quantitative trait loci (QTL) were significantly [P < 0.05, likelihood of odds (LOD) > 2.5] associated with seed yield in at least one set with two significant across all sets. For nine of the yield QTL, the LG82-8379 alleles were associated with yield increases of 1.7 to 5.4% while the BSR 101 alleles increased yield 2.4 to 4.4% at six yield QTL. Four yield QTL were associated with significant changes in R8, eight with plant height, and three with seed protein concentration. Additional QTL were identified for R8, plant height, lodging, and seed protein and oil concentration. These results indicate that soybean PIs have the genetic potential for improving seed yield of U.S. soybean cultivars.

Convergence to the coalescent with simultaneous multiple mergers

The general coalescent process with simultaneous multiple mergers of ancestral lines was initially characterized by Möhle and Sagitov (2001) in terms of a sequence of measures defined on the finite-dimensional simplices. A more compact characterization of the general coalescent requiring a single probability measure Ξ defined on the infinite simplex Δ was suggested by Schweinsberg (2000). This paper presents a simple criterion of weak convergence to the Ξ-coalescent. In contrast to the earlier criterion of Möhle and Sagitov (2001) based on the moment conditions, the key condition here is expressed in terms of the joint distribution of the ranked offspring sizes. This criterion interprets a vector in Δ as the ranked fractions of the total population size assigned to sibling groups constituting a (rare) generation, where a merger might occur. An example of the general coalescent is developed on the basis of the Poisson–Dirichlet distribution. It suggests a simple algorithm of simulating the Kingman coalescent with occasional (simultaneous) multiple mergers.

A comparative study of the porin genes encoding VDAC, a voltage-dependent anion channel protein, in Anopheles gambiae and Drosophila melanogaster

The protein called voltage-dependent anion-selective channel (VDAC), or mitochondrial porin, forms channels that provide the major pathway for small metabolites across the mitochondrial outer membrane. We have identified and sequenced agporin, a gene of the malaria vector mosquito Anopheles gambiae that conceptually encodes a protein with 73% identity to the VDAC protein encoded by the porin gene in Drosophila melanogaster. By in situ hybridization, we have localized agporin at region 35D on the right arm of A. gambiae chromosome 3, which is homologous to the 2L chromosomal arm of D. melanogaster where the porin gene resides. The comparison of agporin with its putative Drosophila counterpart revealed that both the nucleotide sequence and the structural organization of the two genes are strikingly conserved even though the ancestral lines of A. gambiae and D. melanogaster are thought to have diverged about 250 million years ago. Our results suggest that, while in yeast, plants, and mammals, VDAC isoforms are encoded by small multigene families and are able to compensate for each other at least partially, in A. gambiae a single gene encodes the VDAC protein.

Macroevolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences

The phylogenetic relationships among the Drosophila melanogaster group species were analyzed using approximately 1700 nucleotide-long sequences of the mitochondrial DNA. Phylogenetic analysis was performed using this region consisting of a part of the cytochrome b ( cytb) coding gene, the entire coding sequences of tRNA-Leu, tRNA-Ser and the first subunit of NADH dehydrogenase (NADH1), and a part of the 16S-rRNA gene. The study of these sequences showed that this region of mtDNA is very invariable, as regards with the type of the genes that it contains, as well as the order that they are located on it. The resulting phylogenetic trees reveal a topology that separates the species into three main ancestral lines, leading to the following subgroups: (a) ananassae subgroup, (b) montium subgroup, and (c) melanogaster and Oriental subgroups. The inferred topology complements and generally agrees with previously proposed classifications based on morphological and molecular data.