Barley Grain Development during Drought Stress: Current Status and Perspectives

Barley (Hordeum vulgare L.) belongs to small grain cereals that cover more than 78% of the daily calorie consumption of humans. With a prediction of 9.7 billion humans in 2050 (FAO stats) and climatic changes, the question of increasing small grain cereal’s production has become an agricultural challenge. Drought exerts a strong environmental pressure, causing large yield losses worldwide. Therefore, understanding the mechanisms responsible for grain development from the fertilization to the mature dry grain is essential to understand how drought can affect this developmental program. In this book chapter, we present the physiological, molecular and hormonal regulation of barley grain development. In a second part, we describe the consequences of drought at different stage of barley development, with a special focus on the reproductive phase. Finally, in the last part, we present the different methods used to decipher new genetic information related to drought-tolerance. All this knowledge contributes to understanding the tolerance mechanisms of barley and to developing breeding strategies aiming to bring about new varieties with sustained yield in harsh conditions

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

Genetic diversity measures in P. terebinthus: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 119 polymorphic SSR loci. (DOCX 38 kb

Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT)

In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.</p

Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT)

In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.</p

Evaluation of growth and nutritional value of Brassica microgreens grown under red, blue and green LEDs combinations

39 p.-7 fig.-2 tab.-9 tab. supl.Microgreens are rich functional crops with valuable nutritional elements that have health benefits when used as food supplements. Growth characterization,nutritional composition profile of 21 varieties representing five species of the Brassica genus asmicrogreens were assessed under light-emitting diodes(LEDs) conditions. Microgreens were grown under four different LEDs ratios(%); red:blue 80:20 and 20:80 (R80:B20 and R20:B80), or red:green:blue 70:10:20 and 20:10:70 (R70:G10:B20 and R20:G10:B70). Results indicated that supplemental lighting with green LEDs (R70:G10:B20) enhanced vegetative growth and morphology, while blue LEDs (R20:B80) increased the mineral and vitamin contents. Interestingly, by linking the nutritional content with the growth yield to define the optimal LEDs setup, we found that the best lighting to promote the microgreen growth was the green LEDs combination (R70:G10:B20). Remarkably, under the green LEDs combination (R70:G10:B20) conditions,the microgreens of Kohlrabi purple, Cabbage red, Broccoli, Kale Tucsan, Komatsuna red, Tatsoi and Cabbage green, which can benefit human health in conditions with limited food, had the highest growth and nutritional content.This research work is a part of a project received seed funding from the Dubai Future Foundation through the Guaana.com open research platform(grant no. MBR026). Dr. Mortaza is supported from ERDF project “Plants as a tool from sustainable global development” No. CZ.02.1.01/0.0/0.0/16_019/0000827.Peer reviewe

Development of novel ssr markers by next generation sequencing and constructon of the first ssr linkage referance maps in pistachio.

TEZ11526Tez (Doktora) -- Çukurova Üniversitesi, Adana, 2017.Kaynakça (s. 117-128) var.iii, 177 s. : res. (bzs. rnk.), tablo ; 29 cm.Pistacia türleri için literatürde sınırlı sayıda SSR markörleri vardır. Bu nedenle, bu çalışmada yeni nesil sekanslama (NGS) yöntemi ile in silico olarak yeni polimorfik SSR markörler geliştirilmesi ve antepfıstığında ilk SSR tabanlı genetik bağlantı haritalarının oluşturulması amaçlanmıştır. Üç Pistacia vera L. çeşidinden (Siirt, Ohadi ve Bağyolu) ve bir monoik P. atlantica Desf (Pa-18) genotipinden yaklaşık 10x yoğunluğunda elde edilen Illumina sekanslarından polimorfik SSR lokusları elde edilmiştir. Toplam 750 polimorfik SSR lokusu dizayn edilmiş ve 79 adedi (%10.5) yapılan PCR reaksiyonlarında amplifiye olmamıştır. Geri kalan markörler altı P. atlantica genotipi ve 18 P. vera çeşidinde kapiler elektroforez ile polimorfizm bakımından test edilmiştir. Kopleks bant üreten 53 SSR lokusu çalışma kapsamından çıkarılmıştır. Skorlanabilir bant veren toplam 618 SSR primer çiftinden 625 SSR lokusu elde edilmiştir. Gerek bu çalışmadaki gerekse literatürdeki SSR'lar ile Siirt x Bağyolu F1 populasyonu kullanılarak antepfıstığında SSR tabanlı ilk genetik bağlantı haritasını oluşturmak için kullanılmıştır. Ebeveynler, birleştirilmiş ve referans genetik haritalar ayrı ayrı oluşturulmuştur. Birleştirilmiş haritada %70.9’u ortak markör olmak üzere 15 bağlantı grubunda toplam 385 adet markör yer almıştır. Bağlantı gruplarının uzunluğu 61.3 cM (LG8) ile 131.0 cM (LG12) arasında değişmiş ve toplamda 1,511.2 cM uzunluğunda genetik harita elde edilmiştir. Markörler arasındaki uzaklık 3.9 cM ve markör yoğunluğu ise 0.25 olarak hesaplanmıştır. Bu çalışmada geliştirilen yeni SSR markörleri ve oluşturulan genetik haritalar bundan sonra antepfıstığında yapılacak genetik haritalama ve genetik karakterizasyon gibi çalışmalar için referans olacaktır.There are a limited number of simple sequence repeat (SSR) markers in the literature for Pistacia species. Therefore, this study aims to develop novel polymorphic SSR markers in silico by next generation sequencing (NGS) and to construct the first SSR-based genetic linkage maps in pistachio. About 10x coverage of Illumina sequences were obtained from three Pistacia vera L. cultivars (Siirt, Ohadi and Bagyolu) and one monoecious P. Atlantica Desf. genotype (Pa-18) to find polymorphic SSR loci in silico among them. A total of 750 polymorphic SSR loci were detected and 79 (10.5%) did not have amplification in SSRPCR reactions. The remaining loci were tested for polymorphism by capillary electrophoresis in 18 pistachio cultivars in six P. atlantica genotypes. Fifty-three SSR loci produced complex patterns, and they were discarded. A total of 625 SSR loci were produced from 618 SSR primer pairs. The novel SSRs in this study as well as SSRs in the literature were used to construct the first SSR based genetic linkage map of pistachio using Siirt x Bağyolu F1 population. The parental, consensus and reference genetic maps were constructed. The consensus map included 385 SSR markers along with 15 chromosomes and 70.9% of them were common markers. The LG length changed between 61.3 cM (LG8) and 131.0 cM (LG12) with a total length of 1,511.2 cM. The avarage distance between the markers was 3.9 cM, and the marker density was 0.25. The novel SSR markers and constructed genetic linkage maps in this study will be reference for further genetic linkage mapping and genetic characterization studies in pistachio.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: TÜBİTAK-TOVAG 113 O 962, FUK-2014-2637 ve FDK-2015-3641

Development of multiplex Real-time PCR assays for screening of genetically modified organisms (GMOs).

TEZ9541Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2012.Kaynakça (s. 45-48) var.xi, 49 s. : res., tablo ; 29 cm.Ticari değeri olan genetiği değiştirilmiş organizmaların (GDO) sayısı ve bunları belirlemek için geliştirilen moleküler teknikler sürekli değişmektedir. Bunun sonucunda GDO laboratuvarları ve gıda üretim endüstrisi ham materyallerde ve kompleks işlenmiş gıda ürünlerinde güvenilir farklı yöntemleri uygulamaya zorlanmaktadır. Bu çalışmada GDO analizlerinde çoğunlukla kullanılan 35S (karnabahar mozaik virüs promotörü), NOS (Agrobacterium tumefaciens’in nopalin sentez geni terminatörü), FMV (Sıracaotu mozaik virüsünün 35S promotörü) ve Bar (Streptomyces hygroscopicus toprak bakterisi) genlerini belirlemek için çoklu realtime PCR sistemlerinin geliştirilmesi amaçlanmıştır. Bunlara ek olarak, PCR reaksiyonlarında engelleyici bir maddenin olup olmadığını kontrol edebilmek için dahili pozitif kontrol (IPC) ve bitki DNA’sının olup olmadığını belirlemek için bitki spesifik (18sR) probları kullanılmıştır. Real-time PCR reaksiyonlarında üç adet 35S, üç adet NOS, bir adet FMV ve 1 adet Bar genlerinin TaqManTM problarının kombinasyonları test edilmiştir. Sonuç olarak, ikili, üçlü ve dörtlü real-time PCR yöntemleri IPC ve 18sR genlerini içerecek şekilde geliştirilmiştir. Tüm kombinasyonlar hem Applied Biosystem (ABI 7500) hem de Strategene (Mx3005P) firmalarının Real-time PCR cihazlarında yapılmıştır. Geliştirilen yöntemlerin GDO laboratuvarlarında tarama için ucuz ve uygun olduğu bulunmuştur.The number of commerically available genetically modified organisms (GMOs) and molecular detection techniques have been constantly changing. As a result, GMO laboratories and the food production industry currently are forced to apply many different methods to reliably test raw material and complex processed food products. In this study, it was aimed to develop multiplex real-time PCR systems to detect 35S (the promoter of the cauliflower mosaic virüs), NOS (the terminator of the nopaline synthase gene of Agrobacterium tumefaciens), FMV (the 35S promoter from the figwort mosaic virüs), and Bar (from the soilbacterium Streptomyces hygroscopicus) genes as the most widely used in GMO analysis. Additionally an internal positive control (IPC) indicating the presence or absence of PCR inhibiting substances, and plant gene specific primer (18sR) for the detection of plant gene was used in the PCR reactions. Combinations of three 35S, three NOS, one FMV and one Bar TaqManTM probes were tested in Real-time PCR reactions. As a result, duplex, triplex and quadruflex real-time PCR assays were developed including IPC and 18sR genes. All the combinations were performed in both Applied Biosystem (ABI 7500) and Stratagene (Mx3005P) Real-Time PCR systems. The developed methods were found to be inexpensive and suitable for fast screening in GMO labs.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: ZF2012YL5

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)&lt; 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress