Genetic diversity and selection in Puerto Rican horses

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the “Criollo”) horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the “gait-keeper” DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the “gait-keeper” DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant “gait-keeper” allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

GENETIC DIVERSITY OF ANCIENT POPULATIONS IN THE CAUCASUS AND THE ADJACENT STEPPES DURING THE ENEOLITHIC-BRONZE AGE (V-II mill. BC): MAIN RESULTS AND ISSUES OF CULTURAL AND HISTORICAL INTERPRETATION

В статье представлен обзор новейших результатов анализа ДНК древних народов Кавказа и сопредельной степи в эпоху энеолита - бронзы (V-II тыс. до н. э.) и рассматриваются проблемы их культурно-исторической интерпретации. Выделено семь особенностей общей палеогенетической картины региона: 1. Формирование генотипа кавказских охотников-собирателей не позднее XII тыс. до н. э. и его раннее распространение за пределы Кавказа; 2. Существование на Кавказе непрерывной генетической преемственности с эпохи верхнего палеолита; 3. Раннее, не позднее VI тыс. до н. э., появление кавказского и связанного с ним переднеазиатского (иранского и анатолийского) генетического компонента в степном генетическом пуле; 4. Сохранение генетических различий между населением Кавказа и открытой степи на протяжении всей эпохи энеолита - бронзы; 5. Существование вдоль северных склонов Кавказа генетической буферной зоны, которую, в зависимости от исторических и климатических условий, занимали степняки или кавказцы; 6. Односторонняя проводимость потока генов через Кавказ только в направлении с юга на север; 7. Преобладание культурного разнообразия над генетическим. Отмечается, что проблемы культурно-исторической трактовки генетических данных связаны в разной степени с несогласованностью между генетической и археологической таксономиями, недооценкой генетиками археологического контекста и наивной интерпретацией археологами различий в ДНК как культурных атрибутов. The paper provides an overview of the recent DNA analysis of the ancient populations of the Caucasus and the adjacent steppes during the Eneolithic-Bronze Age (V-II mill. BC) and explores the issues of cultural and historical interpretation of the results. Seven specific features of the general paleogenetic picture of the region have been singled out: 1. Development of the genotype of the Caucasian hunters-gatherers not later than 12 000 years ago and its early spread beyond the Caucasus; 2. Existence of genetic continuity in the Caucasus starting from the Upper Paleolithic; 3. Early appearance of the Caucasus and the related Near East (Iranian and Anatolian) genetic component in the steppe genetic pool, not later than VI mill. BC; 4. Preservation of genetic differences between the population of the Caucasus and the steppe population throughout the entire Eneolithic-Bronze Age; 5. Existence of a genetic buffer zone along the northern slopes of the Caucasus occupied either by the steppe population or the Caucasian population depending on historical and climatic conditions; 6. One-way gene flow across the Caucasus only from the south to the north; 7. Predominance of cultural diversity over genetic diversity. It is emphasized that the issues of the cultural and historical interpretation of genetic data are related, in varying degrees, to inconsistency between genetic and archaeological taxonomies, overlooking of the archaeological context by genetic scientists and naive interpretation of differences in DNA as cultural attributes by archaeologists.

SSR and SNP genetic profiling of Armenian grape cultivars gives insights into their identity and pedigree relationships

The South Caucasus is recognised as the primary Vitis vinifera L. (grapevine) domestication centre and has a high diversity of wild and cultivated grapevines. Archaeological findings indicate that winemaking activities have existed in Armenia for more than 6,000 years, viticulture being one of the most important activities of the modern Armenian agricultural sector. Despite this relevance, some grapevines in local collections have not yet been properly identified, thus hindering the efficient conservation, characterisation and eventual use of autochthonous genetic resources. In the present study, a combined SNP and SSR profiling strategy was used for the genetic identification of a series of grapevine accessions from the Grape Collection of the International Academy of Viticulture and Winemaking in Nalbandyan, presumed to be autochthonous Armenian varieties. The results provided useful information for the correct identification of these genetic resources, revealing multiple cases of synonyms, homonyms and misnames. The genetic data made it possible to confirm the pedigree proposed for some of the cultivars identified in this study and to clarify the origin of others. In addition, we propose, for the first time, a series of new trios and duos involving autochthonous Armenian grapevines. The singularity of this genetic pool compared to other Western and Central European varieties, as well as the potential novel sources of variability in traits of interest (e.g., seedlessness) that were found, highlight the importance of improving knowledge of the Armenian grapevine genetic pool.

A ddRADseq Survey of the Genetic Diversity of Rye (Secale cereale L.) Landraces from the Western Alps Reveals the Progressive Reduction of the Local Gene Pool

Rye (Secale cereale L.) has been at the basis of agriculture for centuries in most mountainous and northern areas of Eurasia, because it is more resistant than other cereals to low temperatures and poor soils. Rye deserves to be re-evaluated as a source of “environmentally resilient” genes in the future as well, and particularly in a perspective to grow cereals able to withstand global warming. According to recent studies, modern rye varieties have a relatively narrow genetic pool, a condition that is worsening in the most recent breeding processes. The preservation of local landraces as unique sources of genetic diversity has therefore become important, in order to preserve the genetic heritage of rye. In this study, genetic diversity of rye landraces collected in a sector of the Italian Alps particularly suited to traditional agriculture was investigated using the ddRADseq technique. A few landraces still managed with family farming turned out to be genetically distant from the commercial varieties currently in use, highlighting that the phenomenon of homogenization of the local genetic pool can be still circumvented. Ex situ conservation of genetically divergent landraces is a valid tool to avoid the dissipation of an as yet unexplored genetic potential.

Shell shape as an indicator of phenotypic stocks of Tehuelche scallop (Aequipecten tehuelchus) in Northern Patagonia, Argentina

Tehuelche scallop, Aequipecten tehuelchus, is a commercially exploited species in Northern Patagonia, Argentina. Without genetic differentiation at the species level, A. tehuelchus presents three morphotypes: tehuelchus, madrynensis, and a non-common variant felipponei. The main goal of this study was to analyze the shell shape variation of Tehuelche scallop to differentiate and identify the phenotypic stocks. The shape differences between and within the two main morphotypes (tehuelchus and madrynensis) were assessed using geometric morphometrics in nine localities. The shell shape presented variability at geographic scale, with the morphologic traits that maximized the differentiation among localities between the tehuelchus and madrynensis morphotypes. Scallops from madrynensis morphotype presented higher and circular shell discs with smaller auricles than those from tehuelchus morphotype. Morphometric differentiation was also detected among localities of each morphotype, wherein most of the variability was related to the disc circularity and the symmetry of the auricles. The presence of morphologic variation in San Matias and San Josi gulfs, wherein a single genetic pool is shared, evidenced the plastic nature of the species. Given the distribution of this resource in distinct provincial jurisdictions, the differentiation of phenotypic stocks has relevance in the context of fishery management, especially if zoning and rotational strategies are implemented.

Genetic and viability assessment of a reintroduced Eurasian otter Lutra lutra population on the River Ticino, Italy

On the River Ticino in northern Italy, a small number of captive Eurasian otters Lutra lutra, belonging to the European breeding programme for self-sustaining captive populations, were reintroduced in 1997, after the species had been declared locally extinct in the 1980s. We surveyed for otter signs in 2008, 2010, 2016–2017 and 2018, confirming the presence of what is probably a small population. To assess the abundance and viability of the population, we genotyped fresh spraints collected during the last two surveys, using 11 microsatellite markers, and modelled the population trend using Vortex. A minimum of six individuals were identified from 25 faecal samples. The analysis of mitochondrial DNA determined that the reintroduced otters share a transversion that is characteristic of the Asiatic subspecies Lutra lutra barang, confirming the contribution of the Asiatic subspecies to the genetic pool of the captive-bred founder population. Population size was consistent with the release of three pairs of otters and all models implied that the number of founders was too small to ensure the long-term survival of the population. Stochastic factors are therefore likely to threaten the success of this reintroduction.

Assessment of the genetic diversity and population structure of apricot (Prunus armeniaca L.) germplasm of the Northwestern Himalaya using SSR markers

Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

Redcurrant genetic pool in selection for productivity

We report a study of 23 redcurrant cultivars of different genetic and geographical origin from the All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery’s genetic repository under the conditions of Moscow Region. The cultivar productivity was evaluated against the most important criteria of brush length, number of flowers and inception under contrasting weather conditions. A high cultivar resistance was registered to winter-born injuries and phytopathogens, including powdery mildew (Sphaerotheca morsuvae (Schw.) Berk. et Curt.), Septoria leaf spot (Septoria ribis Desm.) and anthracnose (Pseudopeziza ribis Kleb.). The established productivity under satisfactory weather conditions in growing season ranges from 1.75 (Kaskad) to 3.5 kg berries per bush (Serpantin, Yarkaya, Zametnaya), in most samples averaging to medium values of 2.7-3.0 kg. The inception rate was highest to exceed 60 % in Niva, Asya, Marmeladnitsa, Rote Spatleze, Serpantin, Yarkaya and Zametnaya. The most large-fruited with a 0.75 g average berry weight were Zadunayskaya and Niva cultivars. Serpantin, Yarkaya and Zametnaya originated by the All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery are recommended in selection for productivity for total marketing value, A concise cultivar morphobiological profile, origin, ripening period, chemical fruit composition, vigour and growth descriptions are provided.

Germination, Morphological and Physiological Evaluation of Seedlings Pretreated with Colchicine in Soybean (Glycine max L)

Wider genetic diversity has the potential to improve crop productivity of soybean, especially under environmental stress conditions. The pre-treatment of soybean seeds with antimitotic agents to establish improved genetic pool may also contribute to the enhancement of germination, seedling development, morpho-physiological growth and yield. In this study, 2 soybean genotypes viz. TGx1835-10E and Dundee were imbibed in solutions containing different amounts of colchicine (0.0, 0.1, 0.5 and 1 %) to evaluate the variations in germination, morphometric and physiological parameters. The seeds were imbibed for the period of 12 and 24 h before sowing for germination in plastic pots containing moistened sterile vermiculite. The variance components expressed as means, and mean percentage of total variations showed that colchicine concentration and imbibitional duration were the most important sources of variation for all traits, followed by the genotypes. Significant responses were detected for various germination parameters, seedling morphology and physiological contents such as; chlorophyll content, total phenolics, flavonoids as well as total protein and DNA content in the 2 genotypes used. HIGHLIGHTS Mutagenic pre-treatment of seeds via imbibition Germination and seedling growths of colchicine preconditioned seeds Chloroplastidic pigment analysis of pre-treated seedlings Physiological valuation of primary and secondary metabolites in grown seedlings Role of colchicine on germination, seedling development and growth of soybean plantlets GRAPHICAL ABSTRACT

Flag Leaf Tolerance Study in Moroccan Barley (Hordeum vulgare L.) Varieties Submitted to a Severe Salt Stress

Salt stress is the most significant abiotic stress that can severely limit crop growth and productivity. This problem gets worse in the context of climate change. The Knowledge of genetic pool behavior under such environmental constraints is imperative for growing and research. Here, we tested salt stress tolerance in six barley varieties (‘Amira’, ‘Oussama’, ‘Tamellalet’, ‘Adrar’, ‘Taffa’, and ‘Laanaceur’). To this end, a set of biochemical parameters (chlorophylls, proline, sodium, potassium levels and K+/Na+ ratio) were measured. Salt constraint significantly reduced chlorophyll content and K+/Na+ but resulted in high records of proline and Na+. Our outcomes show that treatment was the main variability since it explained more than 75% in data variability followed by variety effect. Wide variabilities were found among varieties for the measured parameters. Higher proline levels and K+/Na+ were found in ‘Adrar’, ‘Tamellalet’ and ‘Taffa’. These two later varieties also displayed a higher record of K+. Lower Na+ values were recorded in ‘Laanaceur’, ‘Taffa’, and ‘Tamellalet’, indicating their relative resistance against salt stress. In contrast, ‘Oussama’ and ‘Amira’ were relatively salt-sensitive due to their higher Na+ and lowered K+/Na+ and proline content. Resistant varieties could represent a good background for breeding for barley salt tolerance.