Assessment of genomic imprinting of SLC38A4, NNAT, NAP1L5, and H19 in cattle

Background

Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP).

Results

Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied.

Conclusion

We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.     

Farmers Drive Genetic Diversity of Thai Purple Rice (Oryza sativa L.) Landraces

Purple or black rice (Oryza sativa L.) is a culturally important germplasm in Asia with a long history of cultivation in northern Thailand. Purple rice is identified by the color of the rice pericarp, which varies from purple to black with the accumulation of phenolic acids, flavonoids, and anthocyanins. In the present study, we assessed molecular variation within and between wetland purple rice landraces germplasm from northern and northeastern Thailand using 12 microsatellite loci. All purple rice varieties surveyed showed high levels of homozygosity within varieties and strong genetic differentiation among varieties, indicating the fixation of genetic differences among them. This pattern is consistent with purple rice farming practices in northern Thailand, where a small portion of harvested seed is selected and replanted based on farmers’ preferences. The reduced genetic diversity and high homozygosity observed for purple rice is also consistent with patterns expected for this inbreeding crop. Genetic differentiation among the varieties showed some degree of structuring based on their geographical origin. Taken together, these data highlight that the genetic diversity and structure of wetland purple rice landraces is shaped by farmer utilization and cultivation through local cultural practices, and that conservation should focus on ex situ conservation across its cultivation range, along with on-farm, in situ conservation based on farmers’ seed-saving practices. In situ conservation may prove especially valuable for preserving the genetic identity of local varieties and promote adaptation to local environments.

     

芝麻种质资源及相关分子生物学研究进展

芝麻是重要的优质传统油料作物,素有"油料皇后"的美称。我国拥有丰富的芝麻种质资源,深入研究、评价和有效利用芝麻种质资源是保护其遗传多样性、拓宽遗传基础进而提高芝麻产量和品质的关键。本文对芝麻种质资源的收集保存、鉴定评价、利用现状、品种选育概况及相关分子生物学研究进展进行综述,期望能对芝麻遗传及应用研究提供一些参考。     

Effects of monsoon on distribution patterns of tropical plants in Asia

Comparing with other regions, Asia is mostly dominated by the monsoon climate and tropical plants can be found at the furthest places away from the equator. Understanding the role of monsoon in the dispersal and evolution of tropical plants is helpful for exploring the distribution patterns of vegetation and mechanisms underlying the origin and maintenance of biodiversity in Asia. In summer, there are three types of monsoon in Asia, i.e. East Asia Monsoon, South Asia Monsoon, North-west Pacific Ocean Monsoon. The summer monsoon climate in Asia originated at about 40 Ma, when the early angiosperm evolved and started its diversification in Southeast Asia and South China. It suggested that the monsoon may facilitate the quick speciation and spread of early angiosperm. Monsoon climate facilitates the northward spread of Asia’s tropical plants and some tropical plants can be found even at Yarlung Zangbo River and the boundaries of Guizhou-Guangxi-Yunnan. Such effetcs largely change distribution patterns of zonal vegetation and even causes local vegetation types in some places with unusual topography such as tropical seasonal rainforests, monsoon rainforests, savanna and grassland along dry-hot valley in Southwest China, coastal savanna in West Hainan Island. The three summer monsoons interact at Southwest China and Indo-China Peninsula and these regions are dominated by limestone landscapes and high mountains with big rivers. Some Asia-endemic tropical taxa even formed a diversification and endemism center at this region, which may be a reason for the formation and maintenance of Indo-Burma biodiversity hotspots with global warming, the monsoon may further promote the northward spread of tropical plants and may have fundamental effects on biodiversity and flora evolution in South China.     

Modern Hunting Practices and Wild Meat Trade in the Oil Palm Plantation-Dominated Landscapes of Sumatra,Indonesia

The ongoing expansion of plantation agriculture has changed the ecological, demographic, and social conditions of Southeast Asia’s forested areas, yet little is known about hunting practices in these novel landscapes. Using information from 73 in-depth interviews with hunters, agricultural workers and wild meat dealers in the Jambi province of Sumatra, Indonesia, we describe contemporary hunting practices, including how hunting methods, wildlife harvest and consumption rates vary between different indigenous and immigrant ethnic groups. Hunting is now primarily a commercial endeavor for harvesting wild boar (Sus scrofa) meat; over 7500 wild boars were sold in Jambi City alone in 2011. The Muslim majority avoids wild boar for religious reasons, but there is substantial local and export demand driven by Chinese and Christian Batak. We conclude that hunting within oil palm plantations may reduce crop damage from wild boar and also yield large amounts of wild meat with relatively little by-catch of threatened animals.     

660. NUYTSIA FLORIBUNDA

Summary. Nuytsia floribunda (Labill.) R.Br. ex G.Don, a monotypic arborescent root hemiparasite endemic to the Southwest Australian Floristic Region, sister to all other showy mistletoes, is described and illustrated. A review is provided of its mythological and practical use by Noongar Aborigines, its discovery and early documentation by Europeans, and its phylogeny, biology, ecology and systematics. Experiences with its cultivation and propagation before and after it was discovered to be parasitic are discussed. Nuytsia provides a useful case study for testing many hypotheses developed in OCBIL theory, which aims to explain the evolution and ecology of, and best conservation practices for, biota on very old, climatically buffered, infertile landscapes (i.e. OCBILs), found especially in regions such as the Southwest Australian Floristic Region, the Greater Cape of South Africa and the Pantepui of Venezuela.     

Metabolic engineering of fatty acid biosynthetic pathway in sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.): assembling tools to develop nutritionally desirable sesame seed oil

Vegetable oils are an essential component of human diet, in terms of their health beneficial roles. Despite their importance, the fatty acid profile of most commonly used edible oil seed crop plants are imbalanced; this skewed ratio of fatty acids in the diet has been shown to be a major reason for the occurrence of cardiovascular and autoimmune diseases. Until recently, it was not possible to exert significant control over the fatty acid composition of vegetable oils derived from different plants. However, the advent of metabolic engineering, knowledge of the genetic networks and regulatory hierarchies in plants have offered novel opportunities to tailor-made the composition of vegetable oils for their optimization in regard to food functionality and dietary requirements. Sesame (Sesamum indicum L.) is one of the ancient oilseed crop in Indian subcontinent but its seed oil is devoid of balanced proportion of ω-6:ω-3 fatty acids. A recent study by our group has shed new lights on metabolic engineering strategies for the purpose of nutritional improvement of sesame seed oil to divert the carbon flux from the production of linoleic acid (C18:2) to α-linolenic acid (C18:3). Apart from that, this review evaluates current understanding of regulation of fatty acid biosynthetic pathways in sesame and attempts to identify the major options of metabolic engineering to produce superior sesame seed oil.     

Improvement of biological control capacity of Paenibacillus polymyxa E681 by seed pelleting on sesame

Sesame is an important vegetable crop for the production of oil in Korea. The main obstacle of sesame cultivation is the occurrence of damping-off diseases and wilt caused by a complex of soil-borne pathogens in fields cultivated for two or more successive years. To protect sesame seedlings against these diseases, Paenibacillus polymyxa E681, a plant growth-promoting rhizobacterium (PGPR) previously shown to suppress disease incidence and promote growth on cucumber and pepper in the greenhouse and field experiments, was evaluated for its capacity for biological control and growth promotion in vitro and in situ. Seed treatment with strain E681 alone did not show consistent protection. Therefore, seed pelleting with strain E681 was attempted to increase the seed size and improve the stability and effectiveness of biocontrol capacity by strain E681. Through screening of pelleting materials, a combination of clay and vermiculite was selected for further experiments to enhance seed germination and root colonization of strain E681 on sesame. In greenhouse trials, formulations of strain E681 reduced disease incidence in disease-conducive soil. In the field, pelleting of sesame seeds with strain E681 significantly reduced pre- and post-emergence damping-off compared to the non-treated or pelleting alone controls; pelleting also promoted the plant growth and the grain yield. Furthermore, the efficacy of strain E681 for biological control and plant growth promotion was improved by sesame seed pelleting compared to the treatment with strain E681 alone. Hence, the application of strain E681 via seed pelleting offers potential to overcome some of the problems associated with successive years of sesame cultivation.     

Improvement of biological control capacity of Paenibacillus polymyxa E681 by seed pelleting on sesame

Sesame is an important vegetable crop for the production of oil in Korea. The main obstacle of sesame cultivation is the occurrence of damping-off diseases and wilt caused by a complex of soil-borne pathogens in fields cultivated for two or more successive years. To protect sesame seedlings against these diseases, Paenibacillus polymyxa E681, a plant growth-promoting rhizobacterium (PGPR) previously shown to suppress disease incidence and promote growth on cucumber and pepper in the greenhouse and field experiments, was evaluated for its capacity for biological control and growth promotion in vitro and in situ. Seed treatment with strain E681 alone did not show consistent protection. Therefore, seed pelleting with strain E681 was attempted to increase the seed size and improve the stability and effectiveness of biocontrol capacity by strain E681. Through screening of pelleting materials, a combination of clay and vermiculite was selected for further experiments to enhance seed germination and root colonization of strain E681 on sesame. In greenhouse trials, formulations of strain E681 reduced disease incidence in disease-conducive soil. In the field, pelleting of sesame seeds with strain E681 significantly reduced pre- and post-emergence damping-off compared to the non-treated or pelleting alone controls; pelleting also promoted the plant growth and the grain yield. Furthermore, the efficacy of strain E681 for biological control and plant growth promotion was improved by sesame seed pelleting compared to the treatment with strain E681 alone. Hence, the application of strain E681 via seed pelleting offers potential to overcome some of the problems associated with successive years of sesame cultivation.     

High-throughput single nucleotide polymorphism (SNP) identification and mapping in the sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) genome with genotyping by sequencing (GBS) analysis

Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade. There is thus limited knowledge regarding genome-specific molecular markers that are indispensible for germplasm enhancement, gene identification, and marker-assisted breeding in sesame. In this study, we employed a genotyping by sequencing (GBS) approach to a sesame recombinant inbred line (RIL) population for high-throughput single nucleotide polymorphism (SNP) identification and genotyping. A total of 15,521 SNPs were identified with 14,786 SNPs (95.26 %) located along sesame genome assembly pseudomolecules. By incorporating sesame-specific simple sequence repeat (SSR) markers developed in our previous work, 230.73 megabases (99 %) of sequence from the genome assembly were saturated with markers. This large number of markers will be available for sesame geneticists as a resource for candidate polymorphisms located along the physical chromosomes of sesame. Defining SNP loci in genome assembly sequences provides the flexibility to utilize any genotyping strategy to survey any sesame population. SNPs selected through a high stringency filtering protocol (770 SNPs) for improved map accuracy were used in conjunction with SSR markers (50 SSRs) in linkage analysis, resulting in 13 linkage groups that encompass a total genetic distance of 914 cM with 432 markers (420 SNPs, 12 SSRs). The genetic linkage map constitutes the basis for future work that will involve quantitative trait locus (QTL) analyses of metabolic and agronomic traits in the segregating RIL population.     

A new method of propagation of arbuscular mycorrhizal fungi in field cropped sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.)

Though arbuscular mycorrhizal (AM) fungi are indigenous to agricultural soils, their beneficial effects to host plants could be further improved by inoculation with efficient species. The method of AM propagation described in the present study uses oil cake as a supporting medium for the simultaneous delivery of sesame seeds and AM inoculum to the field. Experiment was conducted in a farmer’s field located at Avoor, Kerala, India where sesame was cultivated as a winter crop in rice fallows. Oil cake entrapped with sesame seeds (var. Tilatara) and AM fungus (Funneliformis dimorphicus) inoculum was prepared by thoroughly mixing sterilized coconut cake and neem cake (5:1 v/v), surface sterilized sesame seeds and sterilized spore sieving of F. dimorphicus from a pot culture in a 10% solution of a polysaccharide gum obtained from the seeds of Strychnos potatorum L. Entire mix was moulded into 2.5 cm cubes (ca. 5g) containing approximately 25–30 seeds and 200–300 spores cube^?1 and shade dried before application. The cubes were broadcast @ 600 kg ha^?1 in inoculated treatments. In uninoculated treatments, the oil cake cubes devoid of the fungal component was used. Harvested root samples from the inoculated treatments showed a high frequency (%F) and intensity (%M) of colonization by AM fungi as well as frequency of vesicles (%V) and arbuscules (%A) compared to uninoculated control. The growth (root length, shoot length and leaf area) and yield characters (pod number, seed number, seed weight and oil content) of sesame plants were significantly (p=0.05) improved under the present method of AM propagation indicating its viability under field condition.     

Seed-specific increased expression of 2S albumin promoter of sesame qualifies it as a useful genetic tool for fatty acid metabolic engineering and related transgenic intervention in sesame and other oil seed crops

The sesame 2S albumin (2Salb) promoter was evaluated for its capacity to express the reporter gusA gene encoding β-glucuronidase in transgenic tobacco seeds relative to the soybean fad3C gene promoter element. Results revealed increased expression of gusA gene in tobacco seed tissue when driven by sesame 2S albumin promoter. Prediction based deletion analysis of both the promoter elements confirmed the necessary cis-acting regulatory elements as well as the minimal promoter element for optimal expression in each case. The results also revealed that cis-regulatory elements might have been responsible for high level expression as well as spatio-temporal regulation of the sesame 2S albumin promoter. Transgenic over-expression of a fatty acid desaturase (fad3C) gene of soybean driven by 2S albumin promoter resulted in seed-specific enhanced level of α-linolenic acid in sesame. The present study, for the first time helped to identify that the sesame 2S albumin promoter is a promising endogenous genetic element in genetic engineering approaches requiring spatio-temporal regulation of gene(s) of interest in sesame and can also be useful as a heterologous genetic element in other important oil seed crop plants in general for which seed oil is the harvested product. The study also established the feasibility of fatty acid metabolic engineering strategy undertaken to improve quality of edible seed oil in sesame using the 2S albumin promoter as regulatory element.     

Stable Carbon Isotope Evidence for Neolithic and Bronze Age Crop Water Management in the Eastern Mediterranean and Southwest Asia

In a large study on early crop water management, stable carbon isotope discrimination was determined for 275 charred grain samples from nine archaeological sites, dating primarily to the Neolithic and Bronze Age, from the Eastern Mediterranean and Western Asia. This has revealed that wheat (Triticum spp.) was regularly grown in wetter conditions than barley (Hordeum sp.), indicating systematic preferential treatment of wheat that may reflect a cultural preference for wheat over barley. Isotopic analysis of pulse crops (Lens culinaris, Pisum sativum and Vicia ervilia) indicates cultivation in highly varied water conditions at some sites, possibly as a result of opportunistic watering practices. The results have also provided evidence for local land-use and changing agricultural practices.     

Subsistence benefits from the babassu palm (Orbignya martiana)

Stands of babassu palms (Orbignya martiana) occupy an area of Brazil estimated at nearly 200,000 km², concentrated in the states of Maranhão, Piauí and Goiás. Babassu’s cryptogeal germination, establishing the apical meristem of the plant below ground for its early growth and development, enables it to survive human disturbance, making the palm an integral part of shifting cultivation and pastoral farming systems. People obtain a multitude of products from babassu throughout the palm’s life cycle: leaves are used widely for thatch, basketry, and construction; trunks for palmito and bridges; the fruit for feed, oil and, charcoal. As many as 450,000 subsistence-level households rely on the sale of babassu kernels, used in a regional vegetable oil industry, for an important share of their cash incomes. Deforestation pressures and technological innovation toward an industry based on mechanical processing of whole babassu fruit threaten to reduce benefits the palm provides to the region’s rural poor. Understanding how babassu is used by rural families who depend upon it will help to make current efforts at “domesticating” the palm and whole-fruit processing more responsive to human needs.     

Job’s-tears (coix lacryma-jobi)—a minor food and fodder crop of northeastern India

Job’s-tears—a cultigen of great antiquity—is grown in South Asia mainly by the natives of various ethnic groups of Mongolian origin. The plant is used as a minor cereal and fodder. The northeastern region of India is a centre of variability for the genus Coix. It is considered that this plant was introduced here either by the pestoral Aryan invaders, who grew it on the slopes of the Himalayas or during Mongolian conquests when the crop got distributed from the eastern Himalayas to lower subtropical terrains. During plant explorations conducted since 1970 in the northeastern region of India, much variability has been recorded for this crop. The various soft-shelled races now grown in this tract by the tribes are the result of conscious folk domestication and must have been selected for easy hulling and good kernel type. Based on this, and on information on domestication, cultivation and economic usages of this plant among the natives, some findings are presented in this paper.     

Molecular dynamics of interaction of Sesamin and related compounds with the cancer marker β-catenin: an in silico study

By virtue of their regulatory role in the biological process, certain protein–protein complexes form potential targets for designing and discovery of drugs. Alteration set in the controlled formation of such complexes results in dysregulation of several metabolic processes, leading to diseased condition. β-catenin/Tcf4 complex is one such protein–protein complex found altered in colorectal epithelial cells resulting in activation of target genes leading to cancer. Recently, certain lignans from seeds of the oil crop sesame were found inhibiting initiation and progression of this type of cancer. Molecular mechanism involved in the process, however, is not yet known. By an in silico study, we present here a possible mechanism of interaction between the sesame lignans and β-catenin leading to inhibition of formation of the said complex, thereby elevating some of these ligands as potential lead molecules in the development of drugs for treatment of colon cancer. To achieve this objective, we performed docking, molecular dynamics simulation, and binding free energy analysis of target–ligand complexes. Using computational alanine scanning approach, the key pocket residues of β-catenin that interact with Tcf4 in the formation of complex were identified. The test molecules were initially evaluated for their drug-like properties by application of Lipinski’s rule of five. Results of this study revealed that Sesamin, a furofuran lignan from sesame, has the highest affinity for β-catenin particularly with its residues that interact with Tcf4 and thus serving as a potential lead molecule for development of a drug for colon cancer.     

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference‐assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan‐genome of 554.05 Mb. The pan‐genome contained 26 472 orthologous gene clusters; 15 409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11 063) clusters and the 15 890 variety‐specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant‐pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan‐genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement.     

Biosynthesis of medium chain length poly(3-hydroxyalkanoates) (mcl-PHAs) by Comamonas testosteroni during cultivation on vegetable oils

Comamonas testosteroni has been studied for its ability to synthesize and accumulate medium chain length poly(3-hydroxyalkanoates) (mcl-PHAs) during cultivation on vegetable oils available in the local market. Castor seed oil, coconut oil, mustard oil, cotton seed oil, groundnut oil, olive oil and sesame oil were supplemented in the mineral medium as a sole source of carbon for growth and PHAs accumulation. The composition of PHAs was analysed by a coupled gas chromatography/mass spectroscopy (GC/MS). PHAs contained C6 to C14 3-hydroxy acids, with a strong presence of 3-hydroxyoctanoate when coconut oil, mustard oil, cotton seed oil and groundnut oil were supplied. 3-hydroxydecanoate was incorporated at higher concentrations when castor seed oil, olive oil and sesame oil were the substrates. Purified PHAs samples were characterized by Fourier Transform Infrared (FTIR) and 13C NMR analysis. During cultivation on various vegetable oils, C. testosteroni accumulated PHAs up to 78.5-87.5% of the cellular dry material (CDM). The efficiency of the culture to convert oil to PHAs ranged from 53.1% to 58.3% for different vegetable oils. Further more, the composition of the PHAs formed was not found to be substrate dependent as PHAs obtained from C. testosteroni during growth on variety of vegetable oils showed similar compositions; 3-hydroxyoctanoic acid and/or 3-hydroxydecanoic acid being always predominant. The polymerizing system of C. testosteroni showed higher preference for C8 and C10 monomers as longer and smaller monomers were incorporated less efficiently.