Quantitative Trait Loci Mapping of Stem oBrix Content and Stem Diameter in Sorghum Recombinant Inbred Lines Using Genotype-By-Sequencing

Sweet sorghum has the ability to store sugar in its stem. Many sugar content genes have been discovered and through breeding worldwide. However, some of these genes are unstable. This study aimed to detect and validate QTL for stem oBrix content from sorghum RILs. In two seasons, QTL linked with stem brix content and related traits were examined using 139 F8RILs from a grain and sweet sorghum. A genetic linkage map with 128 SNP markers was created and several QTLs were identified. Phenotypic variation between 6.33 and 14% was identified for a given trait. Over two seasons, four QTLs for stem brix content (qBrix2-1, qBrix4-1, qBrix4-2, and qBrix10-1) and three QTLs for stem diameter (qSD1-1, qSD8-1 and qSD9-1) were detected. The detected QTL could be useful for improving stem brix content in different growing season. Furthermore, it makes a significant contribution to marker-assisted brix selection and sorghum biofuel improvement.

Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence

Comparative phylogeography explores the historical congruence of individual species phylogeographic histories to understand the factors that led to their current genetic and phenotypic structures. Various factors can result in currently co-distributed species exhibiting different phylogeographic patterns. The Baja California peninsula and adjacent desert regions provide several potential biogeographic barriers, which have left phylogeographic patterns in some but not all species. We discuss data from bird species found in this region that are relevant to understanding potential biogeographic barriers provided by the Vizcaino Desert. One goal is to compare different sources of molecular data. We show that previous work using mitochondrial markers and single-locus nuclear markers are concordant with similar analyses conducted with genome-wide SNP data (genotype-by-sequencing (GBS) for four bird species found along the Baja California peninsula and adjacent mainland, cactus wren, Gila woodpecker, California gnatcatcher, and LeContes thrasher. The cactus wren and LeContes thrasher show a concordant historical division at or near the Vizcaino Desert in north-central Baja California, the Gila woodpecker appears to be at an intermediate stage of divergence, whereas the California gnatcatcher lacks comparable phylogeographic structure. None of the species we analyzed are classified taxonomically in a way that captures their evolutionary history, with the exception of the LeContes thrasher. The evolutionary division at the Vizcaino desert is well known in other vertebrate species, and our study further corroborates the extent and importance of this biogeographic boundary. The areas north and south of the Vizcaino Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation.

Has the introduction of two subspecies generated dispersal barriers among invasive possums in New Zealand?

The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become one of New Zealand’s most significant pests. Although derived from two subspecies, possums in New Zealand are generally considered to be a single entity. In a previous analysis, we showed that possums in the Hawkes Bay region of New Zealand appeared to consist of at least two overlapping populations. Here, we extend that analysis using a genotype-by-sequencing approach to examine the origins and population structure of those possums and compare their genetic diversity to animals sampled from Australia. We identify two populations of each subspecies in Hawkes Bay and provide clear evidence of a contact zone between them in which a hybrid form is evident. Our analysis of private alleles shows higher rates of dispersal into the contact zone than away from it, suggesting that the contact zone functions as a sink (and hence as a barrier) between the two subspecies. Given the widespread and overlapping distribution of the two subspecies across both large islands in New Zealand, it is possible that many such contact zones exist. These results suggest an opportunity for a more targeted approach to controlling this pest by recognising sub-specific differences and identifying the contact zones that may form between them.

Complex introgression among three diverged largemouth bass lineages

Hybrid zones between diverged lineages offer an unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships between these Mobile Delta bass populations, M. salmoides, and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8,582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.

Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain

Digital polymerase chain reaction (dPCR) is a breakthrough technology based on the partitioning of the analytical sample and detection of individual end-point amplifications into the separate compartments. Among the numerous applications of this technology, its suitability in mutation detection is relevant and characterized by unprecedented levels of precision. The actual applicability of this analytical technique to quantify the presence of a specific plant genotype, in both raw materials and transformed products, by exploiting a point polymorphism has been evaluated. As proof of concept, an Italian premium pasta production chain was considered and a dPCR assay based on a durum wheat target variety private point mutation was designed and evaluated in supply-chain samples. From the results obtained, the assay can be applied to confirm the presence of a target variety and to quantify it in raw materials and transformed products, such as commercial grain lots and pasta. The performance, costs, and applicability of the assay has been compared to analytical alternatives, namely simple sequence repeats (SSRs) and genotype-by-sequencing based on Diversity Arrays Technology sequencing (DArTseqTM).

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (Rubus idaeus L.)

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.

Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in Southwestern Nigeria

Coffee (Coffea spp.) is one of the most popular refreshing beverages globally. Coffee lipid diversity has untapped potential for improving coffee marketability because lipids contribute significantly to both the health benefits and cup quality of coffee. However, in spite of its potential importance, there have not been extensive studies of lipids among C. canephora genotypes. In this study, ultra-performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of lipid molecules was performed for 30 genotypes consisting of 15 cultivated and 15 conserved genotypes of C. canephora in Southwestern Nigeria. We identified nine classes of lipids in the 30 genotypes which belong to the ‘Niaouli’, ‘Kouillou’ and ‘Java Robusta’ group: among these, the most abundant lipid class was the triacylglycerols, followed by the fatty acyls group. Although ‘Niaouli’ diverged from the ‘Kouillou’ and ‘Java Robusta’ genotypes when their lipid profiles were compared, there was greater similarity in their lipid composition by multivariate analysis, compared to that observed when their primary metabolites and especially their secondary metabolite profiles were examined. However, distinctions could be made among genotypes. Members of the fatty acyls group had the greatest power to discriminate among genotypes, however, lipids that were low in abundance e.g. a cholesterol ester (20:3), and phosphotidylethanolamine (34:0) were also helpful to understand the relationships among C. canephora genotypes. The divergent lipid profiles identified among the C. canephora genotypes, correlated with their Single Nucleotide Polymorphism grouping as assessed by genotype-by-sequencing, and will be exploited to improve coffee cup quality.