Hybrid Grapes for a Sustainable Viticulture in South Italy: Parentage Diagram Analysis and Metal Assessment in a Homemade Wine of Chambourcin Cultivar

The aim of this work was to explore a more sustainable approach in the viticulture of Mediterranean countries that could derive from growing hybrid grape varieties inheriting tolerance/resistance characters from the wild vines utilized for their selection. Among the plethora of hybrid grapes developed in the last decades, some are able to produce high-quality wines whose flavor resembles European varieties, thus overcoming a typical limit of several old hybrids based on V. labrusca whose wine was characterized by a distinctive wild flavor. In this context, we examined some characteristics of Chambourcin, one of the most promising hybrid cultivars producing quality red wine and requiring much less phytosanitary interventions than European grapevine. In detail, the scope of this study included the investigation of the parentage diagram for this hybrid grape variety and the chemical analysis of a Chambourcin wine produced in South Italy. We filled the gaps corresponding to some of the Vitis ancestors participating in its complex pedigree by means of a literature analysis and a mathematical approach. We found high ancestry of V. vinifera (about 41%), followed by V. berlandieri (about 28%), V. rupestris (about 19%) and to a lesser extent other American wild vines. The significant content of V. berlandieri and V. rupestris genome in Chambourcin explains the considerable resistance of this variety to the two main pathogens affecting grapevines, i.e., downy mildew and powdery mildew. We then analyzed an organic Chambourcin wine produced in South Italy from grapes obtained without any phytosanitary treatment by Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) in order to assess heavy metal content and found it comparable to other (red and rosè) V. vinifera wines obtained from family-run vineyards. Heavy metals contents detected were not of concern for any of the wines analyzed, however, copper accumulation in V. vinifera vineyard soils, and pollution deriving from other phytosanitary chemicals remain issues that in the case of Chambourcin vineyards could be solved at least in large part.

The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent–offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as “summed potential lengths of shared haplotypes”, SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for ‘Emperor Francis, and ‘Schmidt’, a half-sib relationship for ‘Van’ and ‘Windsor’, and the paternal grandparents of ‘Stella’ were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of ‘Cox’s Pomona’ was reconstructed, and ‘Fameuse’ was deduced to be a likely grandparent of ‘McIntosh’. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

Epigenetic models predict age and aging in plains zebras and other equids

ABSTRACTFive of the seven extant wild species of the genus Equus are species of significant conservation concern. Effective conservation and management of such threatened wildlife populations depends on the ability to estimate demographic trends and population viability and therefore requires accurate assessment of age structure. However, reliably aging wildlife is challenging as many methods are highly invasive, inaccurate, or both. Epigenetic aging models, which estimate individual age with high accuracy based on genomic methylation patterns, are promising developments in this regard. Importantly, epigenetic aging models developed for one species can potentially predict age with high accuracy in sister taxa. Using blood and biopsy samples from known age plains zebras (Equus quagga), we developed epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker (EPM) models to predict biological age. We tested the ability of our blood-based EC to predict ages of Grevy’s zebras, Somali asses and domestic horses, from blood samples. Because our samples came from a population with a complex pedigree, we also leveraged information from a previous sequencing effort to measure the association between levels of inbreeding (F and ROH) and the age acceleration as measured by DNA methylation. The resulting models describe the trajectory of epigenetic aging in plains zebras and accurately predict the ages of plains zebras and other equids. We found moderate support for a slight acceleration of aging with increased inbreeding.

Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’

Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

Genomic consequences of apple improvement

The apple (Malus domestica) is one of the world’s most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of ‘Honeycrisp’, the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars ‘Golden Delicious’ and ‘Red Delicious’ were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple’s future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent

In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between identifying a source for each IBD segment and assembling IBD segments placed within each ancestral individual. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs.We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to the United States from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 10 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 224 ancestral individuals per chromosome. For these ancestral individuals, on average we reconstruct 79% of their haplotypes. We also identify a region on chromosome 16 that is difficult to reconstruct – we find that this region harbors a short Amish-specific copy number variation and the gene HYDIN. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families.Author summaryWhen analyzing complex heritable traits, it is often useful to have genomic data from many generations of an extended family, to increase the amount of information available for statistical inference. However, we typically only have genomic data from the recent generations of a pedigree, as ancestral individuals are deceased. In this work we present an algorithm, called thread, for reconstructing the genomes of ancestral individuals, given a complex pedigree and genomic data from the recent generations. Previous approaches have not been able to accommodate large datasets (both in terms of sites and individuals), made simplifying assumptions about pedigree structure, or did not tie reconstructed sequences back to specific individuals. We apply thread to a complex Old Order Amish pedigree of 1338 individuals, 394 with genotype data.

Others and Brothers

Chapter 1 explores the local language and rhetoric surrounding the idea of sanatana dharma, which roughly translates as “the eternal religion.” Despite the term’s complex pedigree, it more often than not conveys an appeal toward universalism. The author considers it a technique of “brothering,” a concept which indicates that through seeing similarity and downplaying difference, an “other” can become a brother. Tourism serves as a major catalyst in the creation of this discourse, a dynamic epitomized by the repertoire of sayings and phrases promoting Hindu universalism. At the same time, given its place in Pushkar’s tourism economy and its nationalist history, the promise of brotherly love can seem at times tenuous. Here, the author discusses how issues of moneyed interest and virulent nationalism shape, and are negotiated within, discourses of the “eternal religion” while simultaneously giving serious consideration to the prospect of brothering.