Genomic Analysis of Vavilov's Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection.

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain 'genetic gems' with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.

Vavilov's Collection of Worldwide Crop Genetic Resources in the 21st Century.

N.I. Vavilov was among the first scientists who recognized the high potential value of plant genetic resources (PGR) for humankind. In addition to his fundamental work on the centers of crop origin, he emphasized the importance of collection and ex situ conservation of cultivated plants and their wild relatives, to make them available for breeding programs and for future generations. Vavilov's ideas formed a solid scientific basis for the long-term efforts on securing PGR in ex situ genebanks, both internationally and in Russia. The collection of seeds and living plants at the N.I. Vavilov All Russian Institute of Plant Genetic Resources (VIR) is one of the oldest in the world. The size of the collection increased from 301 accessions in 1901 to over 330,000 accessions in 2017, now representing 64 botanical families, 376 genera, and 2169 species. Acquisition was mainly focused on crops that are suitable for cultivation in Russia such as potatoes, barley, wheat, sorghum, beans, vegetables, forage species, and many others. For over a century, VIR has been providing the materials for breeding programs and research, which resulted in developing new cultivars with unique characteristics such as high yield combined with deceased resistance, improved storability, cold and drought tolerance, or ability to grow on deserts and polluted lands. The main field collection near St. Petersburg and 11 main branches across the country covering a wide spectrum of climatic conditions combined with modern seed storage, in vitro and cryobank facilities, and molecular laboratories form a solid platform for breeding, regeneration, and evaluation of accessions in the collection. This article gives a brief overview of VIR as the leading genebank and breeding center in Russia, its main activities in conservation and utilization of PGR for national food security and its role in developing national policies in this area.

Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing.

This article describes how CGIAR centers and partners are using genomic sequence information to promote the conservation and sustainable use of crop genetic diversity, and to generate and share benefits derived from those uses. The article highlights combined institutional, and benefit-sharing-related challenges that need to be addressed to support expanded use of digital sequence information in agricultural research and development.

Embrapa Network for Brazilian Plant Genetic Resources Conservation.

Brazil is one of the most biodiverse countries on Earth, holding ∼10% of the world's vascular plant species. Despite that, Brazilian agriculture is highly dependent on genetic resources originating from other countries. Embrapa (Brazilian Agricultural Research Corporation) is the governmental institution that, since 1973, has been responsible for the introduction and conservation of genetic resources in Brazil. In this article, we report on the experiences that Embrapa has faced over the past 45 years to build and improve a national network for the preservation of plant genetic resources under the coordination of Embrapa Genetic Resources & Biotechnology (CENARGEN), one of the 42 Embrapa decentralized units. The first network-based model, RENARGEN, initiated in 2003, was followed by the National Platform for Genetic Resources (Platform RG) in 2009; and from 2014 until today Embrapa manages the conservation of genetic resources through Portfolio REGEN, in which the plant component is called Plant Genetic Resources Network (RGV). This network covers activities of enrichment, conservation, characterization, and documentation of genebanks. Embrapa's plant genetic resources are conserved in active genebanks (AGs), in long-term seed bank (Colbase), and in vitro and DNA banks. In situ and on-farm conservation are also handled at Embrapa to complement and reinforce ex situ conservation. The latest survey reveals that Embrapa has 134 AGs with ∼150,000 accessions of 1130 plant species, 123,000 accessions of 735 species within Colbase, 1250 in vitro accessions, and 12,000 DNA samples. At least 65% of this collection is documented and available to the public in the Embrapa Alelo system, which also handles quarantine, germplasm exchange, and herbarium data. By the end of 2018, the public Alelo data will be automatically migrated to the Genesys system. In the last 40 years, ∼650,000 accessions have been exchanged by Embrapa, with 70% of them imported from other countries.

Conserving and Sharing Taro Genetic Resources for the Benefit of Global Taro Cultivation: A Core Contribution of the Centre for Pacific Crops and Trees.

This review article gives an account of the origin, domestication, and dispersal of taro, a staple food crop in many countries in the humid tropics and subtropics. Genetic diversity studies indicated that distinct gene pools exist in all the regions where taro may be naturally distributed-the Indian subcontinent, China, Southeast Asia, and in Oceania. The Asian gene pool presented the highest genetic diversity. Diploid taro is prevalent in the Pacific Islands, while both diploids and triploids are found in mainland Asia. Triploids are thought to provide better adaptability and enhanced hardiness to higher altitudes and latitudes where sexual reproduction is not viable. The Centre for Pacific Crops and Trees (CePaCT) conserves in vitro close to 70% of the taro genetic resources held ex situ and is therefore considered the world center for taro genetic resources. Phytophthora colocasiae or taro leaf blight (TLB) is the most severe disease of taro' causing 25%-50% yield losses and postharvest decay of corms. The CePaCT genebank supported the participatory TLB breeding program in Samoa through the provision of diverse taro germplasm from the Asian gene pool. However, CePaCT not only serves taro producers in the Pacific but also shares new allelic diversity of taro globally. More recent distributions of taro genetic diversity to West and Central Africa were in response to an outbreak and spread of TLB in West Africa. Global dissemination of taro genetic diversity is assisting producer countries in the process of adaptation to emerging biotic and abiotic stresses, exacerbated by climate change.

Botanic Gardens Complement Agricultural Gene Bank in Collecting and Conserving Plant Genetic Diversity.

Originating in Europe in the 16th century, botanic gardens are found in nearly every country in the world. Botanic gardens have had various roles during this time, including as physic gardens, as adaptation centers for commercial crops, as pleasure gardens, and more recently as conservation institutions. The role of botanic gardens in the conservation of Crop Wild Relatives is becoming increasingly important. At least 6000 taxa related to 68 crop genera are maintained by the world's botanic gardens with several gardens having specialist collections. The extent of infra-specific genetic diversity of these Plant Genetic Resources for Food and Agriculture (PGRFA) being conserved is currently unknown, although based on existing evidence it is likely to be low. However, these PGRFA collections, through display and education, play a significant role in linking the public to important issues, including food security and the need to conserve crop diversity. Today there are some 2700 botanic gardens in existence, and they are visited by over 500 million people every year. The majority of these gardens are found in temperate regions. At least 30% of all known plant species are found in botanic garden collections, including 41% of threatened species. These ex situ collections are conserved in a variety of ways, including as seed bank collections. Around 350 botanic gardens together maintain seed collections of 57,000 taxa. These seed bank collections have a variety of uses, including for research and reintroduction.

Improving soil seed bank management.

Problems associated with simplified weed management motivate efforts for diversification. Integrated weed management uses the fundamentals of weed biology and applied ecology to provide a framework for diversified weed management programs; the soil seed bank comprises a necessary part of this framework. By targeting seeds, growers can inhibit the propagule pressure on which annual weeds depend for agricultural invasion. Some current management practices affect weed seed banks, such as crop rotation and tillage, but these tools are often used without specific intention to manage weed seeds. Difficulties quantifying the weed seed bank, understanding seed bank phenology, and linking seed banks to emerged weed communities challenge existing soil seed bank management practices. Improved seed bank quantification methods could include DNA profiling of the soil seed bank, mark and recapture, or 3D LIDAR mapping. Successful and sustainable soil seed bank management must constrain functionally diverse and changing weed communities. Harvest weed seed controls represent a step forward, but over-reliance on this singular technique could make it short-lived. Researchers must explore tools inspired by other pest management disciplines, such as gene drives or habitat modification for predatory organisms. Future weed seed bank management will combine multiple complementary practices that enhance diverse agroecosystems. © 2018 Society of Chemical Industry.

KrioBlast TM as a New Technology of Hyper-fast Cryopreservation of Cells and Tissues. Part I. Thermodynamic Aspects and Potential Applications in Reproductive and Regenerative Medicine.

Kinetic (dynamic) vitrification is a promising trend in cryopreservation of biological materials because it allows avoiding the formation of lethal intracellular ice and minimizes harmful effects of highly toxic penetrating cryoprotectants. A uniform cooling protocol and the same instruments can be used for practically all types of cells. In modern technologies, the rate of cooling is essentially limited by the Leidenfrost effect. We describe a novel platform for kinetic vitrification of biological materials KrioBlast TM that realizes hyper-fast cooling and allows overcoming the Leidenfrost effect. This opens prospects for creation of a novel technology of cell cryopreservation for reproductive and regenerative medicine.

Evolving gene banks: improving diverse populations of crop and exotic germplasm with optimal contribution selection.

We simulated pre-breeding in evolving gene banks - populations of exotic and crop types undergoing optimal contribution selection for long-term genetic gain and management of population genetic diversity. The founder population was based on crosses between elite crop varieties and exotic lines of field pea (Pisum sativum) from the primary genepool, and was subjected to 30 cycles of recurrent selection for an economic index composed of four traits with low heritability: black spot resistance, flowering time and stem strength (measured on single plants), and grain yield (measured on whole plots). We compared a small population with low selection pressure, a large population with high selection pressure, and a large population with moderate selection pressure. Single seed descent was compared with S0-derived recurrent selection. Optimal contribution selection achieved higher index and lower population coancestry than truncation selection, which reached a plateau in index improvement after 40 years in the large population with high selection pressure. With optimal contribution selection, index doubled in 38 years in the small population with low selection pressure and 27-28 years in the large population with moderate selection pressure. Single seed descent increased the rate of improvement in index per cycle but also increased cycle time.

Conservation and population genetic diversity of Curcuma wenyujin (Zingiberaceae), a multifunctional medicinal herb.

Curcuma wenyujin is an important multifunctional medicinal herb in China. Currently, populations of C. wenyujin are decreasing, and wild individuals have almost disappeared from their natural habitats. Moreover, little is known regarding the molecular characteristics of this plant. In this study, we investigated the genetic diversity and variation of five populations of C. wenyujin, using ran-dom amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. We found that the percentages of polymorphic loci (PPL) at the species level (98.25% by RAPD and 100% by ISSR) were significantly higher than those at the population level (66.32% by RAPD and 67.14% by ISSR). The highest values of PPL, expected heterozygosity, and Shannon's information index were in Pop1, while the lowest values were in Pop2. Both DNA markers revealed a short genetic distance between Pop1 and Pop2 (0.1424 by RAPD and 0.1904 by ISSR). Phylogenetic trees produced similar results, with Pop1, Pop2, and Pop5 in one group and Pop3 and Pop4 in another. There were no significant correlations between their genetic distances and their geographical distances. The highest genetic diversity was in Pop1 and the lowest was in Pop2, and genetic diversity at the species level was relatively low, but much higher than that at the population level. We recommended the establishment of a germplasm bank, in situ con-servation, and propagation of wild individuals. The present study will improve the evaluation, protection, and utilization of the population resources of C. wenyujin.