Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

<p>Abstract</p> <p>Background</p> <p>A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.</p> <p>Results</p> <p>Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in <it>T. aestivum </it>is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.</p

Plant biotechnology, plant breeding, population biology and genetic resources: perspective from a university scientist

The basic tools for plant biotechnology were developed from the ’50s to the ’80s. For the most part, gene transformation is still in the research phase as the tools are being developed. The future of plant biotechnology, when integrated into agricultural and health sciences looks very promising

Mapping of additive and epistatic QTLs linked to seed longevity in bread wheat (Triticum aestivum L.)

Abstract: Plant genetic resources are stored and regenerated in &gt; 1750 gene banks storing &gt; 7,000,000 accessions. Since seeds are the primary storage units, research on seed longevity is of particular importance. Quantitative trait loci (QTL) analysis of 15 traits related to seed longevity and dormancy using 7584 high-quality SNPs recorded across 2 years and originated from five production years revealed a total of 46 additive QTLs. Exploration of the QTLs with epistatic effect resulted in the detection of 29 pairs of epistatic QTLs. To our information, this is only the second report of epistatic QTLs for seed longevity in bread wheat. We conclude that in addition to dense genetic maps, the epistatic interaction between loci should be considered to capture more variation which remained unnoticed in additive mapping

Mapping of additive and epistatic QTLs linked to seed longevity in bread wheat (Triticum aestivum L.)

Plant genetic resources are stored and regenerated in > 1750 gene banks storing > 7,000,000 accessions. Since seeds are the primary storage units, research on seed longevity is of particular importance. Quantitative trait loci (QTL) analysis of 15 traits related to seed longevity and dormancy using 7584 high-quality SNPs recorded across 2 years and originated from five production years revealed a total of 46 additive QTLs. Exploration of the QTLs with epistatic effect resulted in the detection of 29 pairs of epistatic QTLs. To our information, this is only the second report of epistatic QTLs for seed longevity in bread wheat. We conclude that in addition to dense genetic maps, the epistatic interaction between loci should be considered to capture more variation which remained unnoticed in additive mapping

The General Situation of Wheat Landrace Populations and Factors Affecting Production Decisions of Wheat Landrace Producers in Turkey

Türkiye önemli gen merkezlerinden biri olup aynı zamanda buğdayın anavatanı konumundadır. Anadolu'da 10.000 yıllık bir tarihi olan buğdayın stratejik bir ürün olmasının yanı sıra kültürel bir mirastır. Bu kültürel miras ve genetik çeşitlilik teknolojideki ilerlemeler, girdi kullanımındaki artış, artan nüfus, daha fazla verim ve daha fazla ekonomik kazanç elde edinme isteği gibi nedenlerle yerini yeni modern buğday çeşitlerine bırakmış, yani genetik erozyona uğramıştır. Bu çalışma ile ekim alanları daralmış yerel buğday popülasyonlarını (YBP) üreten üreticilerin bu popülasyonları üretmeye devam etmelerinde etkili olan faktörler ortaya konulmaya çalışılmıştır. Çalışma 2009-2014 yıllarında Gıda, Tarım ve Hayvancılık Bakanlığı, CIMMYT ve ICARDA tarafından koordine edilen IWWIP (International Winter Wheat Improvement Program-Uluslararası Kışlık Buğday Geliştirme Programı) çatısı altında ve son 2 yılında FAO işbirliğinde Türkiye'de 65 ilde yürütülmüştür. "Gayeli Örnekleme Yöntemi" ile belirlenen yerleşim yerlerinde toplam 1873 yerel buğday üreticisi ile yüz yüze anket soru formları doldurulmuştur. Sonuç olarak, Türkiye'de yerel buğday popülasyonlarının hala dağlık ve tarımsal faaliyetlerin daha çok geleneksel sistemlerle yapıldığı alanlarda kendi ihtiyacını karşılamak amacı ile üretilmekte olduğu belirlenmiştir. Geleneksel tat ve lezzet ile hayvancılık faaliyetlerinin bu popülasyonun devam etmesindeki en önemli etkenler olduğu ortaya konulmuşturTurkey is one of the important gene centers and at the same time is the homeland of wheat. Wheat is a strategic product of Anatolia with 10,000 years history, and it is also a cultural heritage. This cultural heritage and genetic diversity have left in their place new modern wheat varieties, thus genetic erosion, increased use of inputs because of technological advances, and socio-economic factors due to increased human population, greater efficiency, and the desire for more economic gain. In this study, we tried to identify factors that are effective in decision-making of the producers of wheat landrace populations whose production areas have narrowed. The study was carried out from 2009 to 2014 in 65 provinces of Turkey under the International Winter Wheat Improvement Program (IWWIP) coordinated by the Ministry of Food, Agriculture and Livestock, CIMMYT and ICARDA and with cooperation with the FAO last two years. The questionnaires forms were completed with 1873 wheat landrace producers by face-to-face interviews in their settlements by the "Purposeful Sampling Method". The major finding was that local wheat populations are still produced in Turkey with the aim of meeting the farmers’ own needs in mountainous areas where agricultural activities are mostly done using traditional systems. It was revealed that traditional taste and flavor of household products, such as bread, and animal husbandry activities were the most important factors in sustaining these wheat landrace population