Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations

As sugarcane is a complex polyaneuploid with many chromosomes, large numbers of markers are required to generate genetic maps with reasonable levels of genome coverage. Comparative mapping was investigated as an approach for both quantitative trait loci (QTL) validation and genetic map enhancement in sugarcane. More than 1000 SSR and AFLP markers were scored in a bi-parental Australian sugarcane population (Q3) that was segregating widely for sugar content-related traits. Two maps were constructed, one for each parent. The Q117 (female) and MQ77-340 (male) maps each contained almost 400 markers distributed onto approximately 100 linkage groups (LGs), of which nearly half could be assigned to homology groups (HGs) on the basis of SSRs. Then, using common SSR and AFLP markers, the two Q3 parental maps were aligned with the maps of the French cultivar, R570, and of the Australian cultivar, Q165^A (A denotes variety covered by Australian plant breeding rights). As a result of comparative mapping, all ten HGs in the Q117 map, and all eleven HGs in the MQ77-340 map could be re-assigned to seven of the expected eight sugarcane HGs, revealing that one sugarcane HG was not covered at all in either Q3 parental map, and that other HGs were poorly represented. QTL analysis in the Q3 population identified approximately 75 marker-trait associations (MTAs) from approximately 18 chromosomal regions or putative QTL in each map for three sugar content-related traits. QTL location appeared to be consistent between the 4 maps; two of the eight HGs were observed to contain MTAs for brix in two or three maps, strongly suggesting the location of sugar content-related trait loci in these HGs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L.

Increasing yield, quality, and disease resistance are important objectives for cacao breeding programs. Yield reduction in material improved for other traits is one of the main constraints caused by self-incompatibility (SI). Genes regulating SI in cacao have not been identified; therefore, knowledge of the location of genetic markers for and the effects of alleles determining SI will be useful for selecting uniformly self-compatible cultivars with higher yields. In a mapping population originating from a cross between a self-incompatible clone, Pound-7, and a self-compatible clone, UF-273, we observed important differences in flower retention at 15, 21, and 28 days after pollination. Our results suggest that the best time to measure flower retention is 15 days after pollination or later and that selecting self-compatibility (SC) thresholds is genotype specific. Using marker-trait association analysis we identified one marker, mTcCIR222, strongly associated with SC, as well as three surrounding markers (mTcCIR168, mTcCIR115 and mTcCIR158), all located near the proximal end of linkage group 4. These markers are currently being tested in our marker-assisted selection program.     

Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces

The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation. In addition, the characterisation of very diversified materials with molecular markers offers a unique opportunity to define significant marker-trait associations of biological and agronomic interest. Here, 50 tomato landraces (mainly collected in central Italy), nine vintage and modern cultivars, and two wild outgroups were grown at two locations in central Italy and characterised for 15 morpho-physiological traits and 29 simple sequence repeat (SSR) loci. The markers were selected to include a group of loci in regions harbouring reported quantitative trait loci (QTLs) that affect fruit size and/or shape (Q-SSRs) and a group of markers that have not been mapped or shown to have a priori known linkage (NQ-SSRs). As revealed by univariate and multivariate analyses of morphological data, the landraces grouped according to vegetative and reproductive traits, with emphasis on fruit size, shape and final destination of the product. Compared to the low molecular polymorphism reported in tomato modern cultivars, our data reveal a high level of molecular diversity in landraces. Such diversity has allowed the inference of the existence of a genetic structure that was factored into the association analysis. As the proportion of significant associations is higher between the Q-SSR subset of markers and the subset of traits related to fruit size and shape than for all of the other combinations, we conclude that this approach is valid for establishing true-positive marker-trait relationships in tomato. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Protein variation accompanies leaf dedifferentiation in sugarcane (Sacchamm officinarum) and is influenced by genotype

Tissue culture lines (morphogenic and nonmorphogenic) were established in five genotypes of Saccharum officinarum L. Changes in protein expression after dedifferentiation of leaf tissue into callus were investigated by two-dimensional gel electrophoresis of cellular proteins. The findings demonstrated that protein expression was regulated both quantitatively and qualitatively in all five genotypes of sugarcane. Sixty-three dedifferention-proteins were identified, of which thirty-three were common to all genotypes. The expression of the remainder was dependent on the genotype, suggesting that the genotype within the same sugarcane species plays an important role in dedifferentiation. Three of the dedifferentiation-proteins were specific to morphogenic callus lines and one to nonmorphogenic callus lines. These proteins can be useful in characterizing the biochemical, molecular, and genetic properties of cultured cells in sugarcane, and in understanding the influence of genotype in the induction of dedifferentiation-proteins and their role in morphogenesis.     

Genetic population structure of sugarcane aphid,Melanaphis sacchari,in sorghum,sugarcane, and Johnsongrass in the continental USA

In 2013, an outbreak of Melanaphis sacchari Zehntner (Hemiptera: Aphididae) was reported in sorghum in Texas, USA. Although this aphid has been reported in the continental USA for nearly a century, its occurrence was limited to Florida and Louisiana sugarcane. After 2013 and within just 3 years M. sacchari was reported in almost all sorghum growing regions from south central to southeastern states in the USA. Sorghum fields in affected areas have sustained considerable losses. This aphid has also been reported on Johnsongrass and other feral grasses. The speed at which this aphid has spread raises serious concerns about future infestations. Many aphid species present genetically distinct populations when feeding on different host plants. Thus, it was hypothesized that the recent outbreak in sorghum could be explained by a recent introduction of a sorghum‐specialized genotype. In this study, we genetically characterized M. sacchari in three of its most common host plants – sorghum, sugarcane, and Johnsongrass – across its geographic distribution in the continental USA. Although M. sacchari specimens were grouped within three genetically distinct clusters, we did not find evidence of host plant or geographic population structure. Our characterization of the genetic structure of this pest provides baseline data aimed to help explain its recent outbreak in sorghum, as well as information that may aid in the design of sustainable control strategies.     

Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana

As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations—that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype–environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype–environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype–environment interaction would increase the amount of genetic variation maintained by mutation‐selection balance.     

Implications of absence of measurement invariance for detecting sex limitation and genotype by environment interaction.

Using univariate sum scores in genetic studies of twin data is common practice. This practice precludes an investigation of the measurement model relating the individual items to an underlying factor. Absence of measurement invariance across a grouping variable such as gender or environmental exposure refers to group differences with respect to the measurement model. It is shown that a decomposition of a sum score into genetic and environmental variance components leads to path coefficients of the additive genetic factor that are biased differentially across groups if individual items are non-invariant. The arising group differences in path coefficients are identical to what is known as "scalar sex limitation" when gender is the grouping variable, or as "gene by environment interaction" when environmental exposure is the grouping variable. In both cases the interpretation would be in terms of a group-specific effect size of the genetic factor. This interpretation may be incorrect if individual items are non-invariant.     

Crop diagnosis and probe genotypes for interpreting genotype environment interaction in winter wheat trials

Genotype*environment interaction has been analyzed with 12 genotypes and four probe genotypes in French wheat trials. An integrated approach was developed which combined crop diagnosis with the analysis of interaction by factorial regression. Crop diagnosis was helpful to characterize the environments and to select environmental variables. Such an approach succeeded in providing an agronomic explanation of genotype*environment interaction and in defining the responses or parameters for each genotype and each environment. Earliness at heading, susceptibility to powdery mildew and susceptibility to lodging were the three major genotypic covariates. Interaction could also be related to environment features, measured indirectly by the behavior of the four probe genotypes during the formation of yield, what we called the outputs of a simplified crop diagnosis, or described directly by indicators of yield-limiting factors. Two important crop diagnosis covariates were analyzed in order to characterize interaction during the formation of yield: the reduction in kernel number, which described the time-period until flowering, and the reduction in thousand kernel weight, which corresponded to the period after flowering. These variates were estimated for each probe genotype and allowed us to compare the behavior of the 12 genotypes to that of the probe genotypes. Both periods of the formation of yield contributed to the interaction, and ’Camp-Rémy’ was the probe of particular interest for the comparisons. When true environmental variates were used, factorial regression revealed that water deficits during the formation of grain number and level of nitrogen were predominant. Such an integrated approach could be exploited when varieties are tested in a network where numerous and diverse yield-limiting factors may occur. Received: 3 August 1998 / Accepted: 16 March 1999     

Temporal and spatial variation in population structure among brooding sea stars in the genus Leptasterias

Temporal genetic studies of low‐dispersing organisms are rare. Marine invertebrates lacking a planktonic larval stage are expected to have lower dispersal, low gene flow, and a higher potential for local adaptation than organisms with planktonic dispersal. Leptasterias is a genus of brooding sea stars containing several cryptic species complexes. Population genetic methods were used to resolve patterns of fine‐scale population structure in central California Leptasterias species using three loci from nuclear and mitochondrial genomes. Historic samples (collected between 1897 and 1998) were compared to contemporary samples (collected between 2008 and 2014) to delineate changes in species distributions in space and time. Phylogenetic analysis of contemporary samples confirmed the presence of a bay‐localized clade and revealed the presence of an additional bay‐localized and previously undescribed clade of Leptasterias. Analysis of contemporary and historic samples indicates two clades are experiencing a constriction in their southern range limit and suggests a decrease in clade‐specific abundance at sites at which they were once prevalent. Historic sampling revealed a dramatically different distribution of diversity along the California coastline compared to contemporary sampling and illustrates the importance of temporal genetic sampling in phylogeographic studies. These samples were collected prior to significant impacts of Sea Star Wasting Disease (SSWD) and represent an in‐depth analysis of genetic structure over 117 years prior to the SSWD‐associated mass die‐off of Leptasterias.     

Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree species

To understand herbivore selection in natural plant populations, it is important to understand the landscape of plant chemical phenotypes that herbivores face and the sources of variation that will define this landscape. We studied the spatial patterns of variation in leaf secondary chemistry of the tropical tree Quararibea asterolepis , Pitt. (Bombacaceae) in a natural population on Barro Colorado Island, Panama, and used this background to discuss hypotheses of natural selection by herbivores. Quararibea plants collected from different sites had consistent differences in their chemical phenotypes. Some of these differences were explained by developmental and environmental sources of variation. Canopy trees had 13% lower yield of leaf extracts than gap seedlings, explained by 41% lower concentrations of the more abundant metabolites in the secondary compound profile. Also, plants growing in gaps had 25% higher yield than those in the understory, explained by two-fold increases in the concentration of some of the less polar secondary compounds in the profile. Differences in soil type did not affect the secondary chemistry of leaves, but sites with different topography had differences in the secondary compound profile that were not explained by any of the measured environmental sources of variation. Neighboring parent-offspring pairs and sibling/half sibling clusters displayed equal or higher variance among themselves than unrelated individuals at farther distances. Assuming that related plants should be more similar in their phenotypes, this pattern is consistent with local selection by herbivores overriding the similarity of related plants in a frequency- or distance-dependent manner.     

Genetic variance of sexually selected traits in waxmoths: maintenance by genotype x environment interaction

When traits experience directional selection, such as that imposed by sexual selection, their genetic variance is expected to diminish. Nonetheless, theory and findings from sexual selection predict and demonstrate that male traits favored by female choice retain substantial amounts of additive genetic variance. We explored this dilemma through an ecological genetic approach and focused on the potential contributions of genotype x environment interaction (GEI) to maintenance of additive genetic variance for male signal characters in the lesser waxmoth, Achroia grisella (Lepidoptera: Pyralidae). We artificially selected genetic variants for two male signal characters, signal rate (SR) and peak amplitude (PA), that influence female attraction and then examined the phenotypic plasticity of these variants (high- and low-SR and high- and low-PA lines) under a range of environmental conditions expected in natural populations. Our split-family breeding experiments indicated that two signal characters, SR and PA, and several developmental characters in both high- and low-SR and high- and low-PA lines displayed considerable phenotypic plasticity among the environments tested. Moreover, strong GEIs leading to crossover between high- and low-SR lines were found for SR and developmental period. Therefore, neither high- nor low-SR genetic variants would achieve maximum attractiveness and fitness in every environment, and those variants producing unattractive signals with low SRs under normal conditions may remain in populations provided that gene flow across environments or generation overlap are sufficiently high. We speculate that the phenotypic plasticity for SR and developmental period is adaptive in A. grisella populations experiencing a range of temperature and density conditions. Females mating with attractive (high-SR) males may be assured of obtaining good genes because these males sire offspring that develop more rapidly and a crossover for developmental period may parallel that for SR. Such parallel crossovers may be expected wherever good-genes sexual selection mechanisms operate.     

Phenotype/genotype associations for yield and salt tolerance in a barley mapping population segregating for two dwarfing genes

Barley traits related to salt tolerance are mapped in a population segregating for a dwarfing gene associated with salt tolerance. Twelve quantitative trait loci (QTLs) were detected for seven seedling traits in doubled haploids from the spring barley cross Derkado x B83-12/21/5 when given saline treatment in hydroponics. The location of QTLs for seedling growth stage (leaf appearance rate), stem weight prior to elongation, and tiller number are reported for the first time. In addition, four QTLs were found for the mature plant traits grain nitrogen and plot yield. In total, seven QTLs are co-located with the dwarfing genes sdw1, on chromosome 3H, and ari-e.GP, on chromosome 5H, including seedling leaf response (SGa) to gibberellic acid (GA(3)). QTLs controlling the growth of leaves (GS2) on chromosomes 2H and 3H and emergence of tillers (TN2) and grain yield were independent of the dwarfing genes. Field trials were grown in eastern Scotland and England to estimate yield and grain composition. A genetic map was used to compare the positions of QTLs for seedling traits with the location of QTLs for the mature plant traits. The results are discussed in relation to the study of barley physiology and the location of genes for dwarf habit and responses to GA.     

Plants in urbanized natural environment: florogenesis,coenogenesis and population structure

Published data on both flora and phytocoenosis genesis and plant population dynamics are reviewed. Urbanized environment is rated as a stress factor for single plants and their communities. The change of plant population structure in cities and towns is analysed as the important indicator of the environment quality. The problems of phytoindication of environment quality in cities and towns for its optimization are considered.     

Genotype by production environment interaction for birth and weaning weights in a population of composite beef cattle

The objectives of the present study were: (1) to evaluate the importance of genotype×production environment interaction for the genetic evaluation of birth weight (BW) and weaning weight (WW) in a population of composite beef cattle in Brazil, and (2) to investigate the importance of sire×contemporary group interaction (S×CG) to model G×E and improve the accuracy of prediction in routine genetic evaluations of this population. Analyses were performed with one, two (favorable and unfavorable) or three (favorable, intermediate, unfavorable) different definitions of production environments. Thus, BW and WW records of animals in a favorable environment were assigned to either trait 1, in an intermediate environment to trait 2 or in an unfavorable environment to trait 3. The (co)variance components were estimated using Gibbs sampling in single-, bi- or three-trait animal models according to the definition of number of production environments. In general, the estimates of genetic parameters for BW and WW were similar between environments. The additive genetic correlations between production environments were close to unity for BW; however, when examining the highest posterior density intervals, the correlation between favorable and unfavorable environments reached a value of only 0.70, a fact that may lead to changes in the ranking of sires across environments. The posterior mean genetic correlation between direct effects was 0.63 in favorable and unfavorable environments for WW. When S×CG was included in two- or three-trait analyses, all direct genetic correlations were close to unity, suggesting that there was no evidence of a genotype×production environment interaction. Furthermore, the model including S×CG contributed to prevent overestimation of the accuracy of breeding values of sires, provided a lower error of prediction for both direct and maternal breeding values, lower squared bias, residual variance and deviance information criterion than the model omitting S×CG. Thus, the model that included S×CG can therefore be considered the best model on the basis of these criteria. The genotype×production environment interaction should not be neglected in the genetic evaluation of BW and WW in the present population of beef cattle. The inclusion of S×CG in the model is a feasible and plausible alternative to model the effects of G×E in the genetic evaluations.     

Microsatellite variation, population structure, and bottlenecks in the threatened copperbelly water snake

Habitat loss and isolation is pervasive in the Midwest U.S. Wetlands are experiencing particularly dramatic declines, yet there is a paucity of information on the genetic impacts of these losses to obligate wetland vertebrates. We quantified the genetic variation of extant populations of a shallow wetland specialist and evaluated potential reductions in population size (i.e. bottlenecks) using seven polymorphic microsatellite DNA markers. We analyzed 228 copperbelly water snakes (Nerodia erythrogaster neglecta), representing populations from three states. Moderate genetic differentiation exists among all three regions (F _ST = 0.12, P < 0.001), with evidence for low levels of differentiation within the federally protected Ohio region (F _ST = 0.025, P = 0.007), and moderate to strong differentiation within the Indiana region (F _ST = 0.23, P < 0.001). Furthermore, Bayesian clustering (i.e. STRUCTURE) supports the separation of the Indiana sites, both from each other and from all other sampling sites. However, it does not support the separation of the Ohio sites from the Kentucky sites. Differentiation among sampling sites did not appear to be related to geographic distance, but rather depended on the quality of terrestrial corridors used for dispersal. Mode shifts in allele frequencies and excess heterozygosity tests were negative, while M-ratio tests were nearly all positive, indicating the likelihood of historical rather than contemporary population bottlenecks. However, potential subspecific intergradation in the Kentucky region may have artificially lowered the M-ratio, and we suggest caution when using the M-ratio approach if intergradation is suspected. Our results have conservation implications for wetland management and management of the copperbelly populations, and emphasizes the importance of protecting wetland complexes.