Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding

Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world. Copyright © 2023 Baloch, Altaf, Liaqat, Bedir, Nadeem, Cömertpay, Çoban, Habyarimana, Barutçular, Cerit, Ludidi, Karaköy, Aasim, Chung, Nawaz, Hatipoğlu, Kökten and Sun

A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris

Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification

Buğdayda (Triticum aestivum L.) bazı önemli tarımsal karakterlerin QLT haritalanması.

TEZ9852Tez (Doktora) -- Çukurova Üniversitesi, Adana, 2012.Kaynakça (s. 159-185) var.xvi, 200 s. : res. (bzs. rnk.), tablo ; 29 cm.Bu araştırma, ekmeklik buğdayda başak ile ilgili kantitatif özellik gen lokuslarının genetik olarak ortaya çıkartılması ve bunların kalıtım şekillerinin anlaşılması amacıyla 2009- 2011 yılları arasında sürdürülmüştür. Türk ekmeklik buğday çeşidi Gerek ile Fas ekmeklik buğday çeşidi Arrehane’nin melezlenmesi ve elde edilen melezlerden tek tohum yöntemiyle olu şturulan rekombinant kendilenmiş hatlarda SSR markerlarla desteklenmiş DArT markerları kullanılarak genetik bağlantı haritası oluşturulmuştur. Bu harita 21 buğday kromozomu üzerinde toplam 935.629 cM uzunluğundaki 54 bağlantı grubundan oluşmuştur. Haritalanan marker sayısı kromozomlara bağlı olarak 5 ile 87 arasında değişmiştir. Farklı kromozomlarda daha önce kromozom üzerindeki yeri bilinmeyen 77 DArT markerı haritalanmıştır. 23 DArT markerının farklı kromozomlar üzerindeki yeri ise daha önce literatürde bildirilen yerlerinden farklı olarak saptanmıştır. Tarımsal ve başak özellikleri ile ilgili kantitatif özellik lokuslarını (QTL) saptamak amacıyla incelenen rekombinant kendilenmiş hatların dört farklı çevrede yetiştirilmesiyle elde edilen morfolojik ve fenolojik veriler ve ba ğlantı haritalarından yararlanılarak QTL haritalaması yapılmıştır. QTL analizleri sonucu 120 QTL belirlenmiştir. Başak morfolojisi ile ilgili çok sayıda yeni ve önemli genomik bölgeler saptanmıştır. Ayrıca, saptanan QTL’lerin bazıları farklı kalite özellikleri için pleiotropik etki göstermiştir. 1A, 1B, 2B, 3D ve 6 B kromozomları üzerinde 1000 dane ağırlığı, başak uzunluğu, başak başına başakçık sayısı, başak başına dane sayısı, başak başına dane ağırlığı , başak sıklığı ve çiçeklenme zamanını etkileyen stabil QTL grupları tanımlanmıştır. Araştırma sonuçlarına dayanarak, DNA markerlarının başak ile ilgili özellikler için arzu edile allelerin frakans ını markera dayalı seleksiyon yoluyla artırma olanağı sağlayabileceği sonucuna varılmıştır .This research was conducted to genetically dissect the quantitative trait loci (QTLs) for spike related and other agronomic traits, and to understand their mode of inheritance in bread wheat during the years of 2009-2011. A genetic linkage map was constructed based on recombinant inbred lines (RILs) derived from cross between the Turkish cultivar Gerek and Moroccon cultivar Arrehane by using DArT markers anchored with SSR markers. This map consisted of 54 linkage groups belonging to twenty one bread wheat chromosomes, spanning to a total of 935.629 cM. Total number of markers mapped varied from 5 to 87 depending on the chromosomes. Seventy seven DArT markers with unpublished chromosomal locations were mapped on different chromosomes, whereas 23 DArT markers were mapped on different chromosomes instead of their published chromosomal locations. Interval mapping was conducted to identify QTLs for agronomic and spike related traits by using four different environments/locations. The QTL analysis led to the detection of 120 QTLs. Several important and novel genomic regions for spike morphology were detected. In addition, some of the QTLs showed pleiotropic effects for different quality traits. Stable QTL clusters influencing the 1000 grain weight, spike length, number of spikelets per spike, number of grains per spike, grain weight per spike, spike compactness and flowering time were identified on chromosomes 1A, 1B, 2B, 3D and 6B. It was concluded that DNA markers might provide an opportunity for increasing the frequency of desirable alleles for spike related traits through marker assisted selection.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: ZF2009D28

Allelic variations of glutenin subunits and their association with quality traits in bread wheat genotypes

The present study was conducted to evaluate the genotype × environment interaction of the yield and quality traits for five bread wheat varieties commonly grown in the Southeastern Anatolia Region of Turkey and 20 advanced lines developed within the framework of the International Winter Wheat Improvement Project. We also determined the allelic pattern of the Glu-1 and Glu-3 loci of these genotypes and examined whether these loci had an effect on the quality traits. There was a significant variation among the genotypes and environments in terms of grain yield, protein content, sedimentation volume (SV), and the extensograph dough energy value (EDEV). The results of the study indicated that genotypic effect was more influential on SV and EDEV than environmental effect; thus, both traits could be used in breeding programs to develop elite cultivars with better quality. Twelve different high-molecularweight (HMW) glutenin alleles were identified at the Glu-A1, Glu-B1, and Glu-D1 loci, resulting in 14 allelic combinations, and 17 different alleles were observed in 19 combinations for low-molecular-weight (LMW) subunits. Furthermore, among all the genotypes, 13 + 16 and 13 + 19 alleles at Glu-B1 and 5 + 12 at Glu-D1 were observed to have the lowest frequency. Our study indicated that the combinations of HMW glutenin alleles with 2* at Glu-A1, 17 + 18 and 13 + 16 at Glu-B1, and 5 + 10 at Glu-D1, as well as the combinations of LMW alleles with subunits c and d at Glu-A3; subunits d, b, c, and g at Glu-B3; and subunits a and b at Glu-D3 had positive effects on the quality traits.The present study was conducted to evaluate the genotype × environment interaction of the yield and quality traits for five bread wheat varieties commonly grown in the Southeastern Anatolia Region of Turkey and 20 advanced lines developed within the framework of the International Winter Wheat Improvement Project. We also determined the allelic pattern of the Glu-1 and Glu-3 loci of these genotypes and examined whether these loci had an effect on the quality traits. There was a significant variation among the genotypes and environments in terms of grain yield, protein content, sedimentation volume (SV), and the extensograph dough energy value (EDEV). The results of the study indicated that genotypic effect was more influential on SV and EDEV than environmental effect; thus, both traits could be used in breeding programs to develop elite cultivars with better quality. Twelve different high-molecularweight (HMW) glutenin alleles were identified at the Glu-A1, Glu-B1, and Glu-D1 loci, resulting in 14 allelic combinations, and 17 different alleles were observed in 19 combinations for low-molecular-weight (LMW) subunits. Furthermore, among all the genotypes, 13 + 16 and 13 + 19 alleles at Glu-B1 and 5 + 12 at Glu-D1 were observed to have the lowest frequency. Our study indicated that the combinations of HMW glutenin alleles with 2* at Glu-A1, 17 + 18 and 13 + 16 at Glu-B1, and 5 + 10 at Glu-D1, as well as the combinations of LMW alleles with subunits c and d at Glu-A3; subunits d, b, c, and g at Glu-B3; and subunits a and b at Glu-D3 had positive effects on the quality traits

Ekmeklik buğdayda (Triticum aestivum L. em Thell) danenin bazı fiziksel özelliklerinin genetik analizi

Buğdayda danenin fiziksel özelliklerinin genetik yapısı hakkındaki bilgiler sınırlıdır. Danenin fiziki yapısı, buğdayın öğütme ve pişirme kalitesi üzerinde doğrudan ya da dolaylı olarak etkiye sahiptir. Bu nedenle danenin fiziksel özelliklerinin kalıtımı hakkında bilgiler dane kalitesi daha yüksek çeşitlerin geliştirilmesinde faydalı olacaktır. Danenin fiziksel özellikleri arasındaki ilişkiler, kalıtım mekanizması ve uyum yeteneğini değerlendirmek için beş ekmeklik buğday çeşidi diallel olarak melezlenmiştir. Uyum yeteneği için yapılan varyans analizi, incelenen özelliklerin çoğu için hem eklemeli hemde epistatik gen etkisi tarafından kontrol edildiğini göstermiştir. Genel uyum kabiliyeti (GCA) değeri, dane yüksekliği (DY) ve dane ağırlığı (DA) haricindeki tüm özellikler için özel uyum kabiliyeti (SCA) değerinden daha yüksek bulunmuştur. GCA:SCA oranına göre incelenen on özelliğin sekizinde GCA daha fazla olmuştur. Path analizi sonuçlarına göre, dane genişliği (DG), başaktaki dane sayısı (BDS) ve dane yüksekliği (DY) diğer özellikler üzerinde doğrudan ve dolaylı etkisinin olduğunu saptanmıştır. Elde edilen bu sonuçlar, buğdayın pişirme ve öğütme kalitesini geliştirmek için, daha iyi dane özelliklerine sahip yeni çeşitleri geliştirmeye çalışan buğday ıslahçılarına faydalı olabilir.Very little information exists on the relative genetic architecture of the grain physical properties of wheat. The physical properties of grain have a direct or indirect influence on the milling and baking quality of wheat. Therefore, understanding the inheritance of grain physical properties will be useful to improve varieties with better quality. Five bread wheat cultivars were crossed in order to evaluate the mode of inheritance and combining ability and the correlation of the grain's physical properties. Analysis of variance for combining ability showed that both additive and non-additive gene actions were involved in controlling most of the traits. Magnitudes of general combining ability (GCA) for all features except grain weight (GW) and grain height (GH) were higher than those of specific combining ability (SCA) The effect of general combining ability was more prominent for 8 out of 10 traits in accordance with ratio of GCA:SCA. Path coefficient analysis showed that grain width (GWI), number of grains per spike (GS), and grain height (GH) had the highest significant direct and indirect effect on most of the other features. The results obtained from this study might be helpful for wheat breeders trying to develop new varieties with better grain features to improve the milling and baking quality of wheat

Genetic Variation for Biofortifying The Maize Grain

The maize germplasm variation is valuable for breeders to develop elite hybrids with increased mineral contents in the maize grain to eliminate mineral malnutrition, which is referred as HIDEN HUNGER. Therefore, we aimed to determine mineral element diversity of maize landraces collected from different geographical regions of Turkey. There was huge diversity for all mineral traits and other quality traits. Turkish maize landraces showed high variation for Zn (17-41.34 mg kg-1), Fe (13.52-29.63 mg kg-1), Cu (0.77-3.34 mg kg-1), Mn (5.68-14.78 mg kg-1), Protein (6.6-11.6%), starch content (73.3-80.0%), oil content (3.15-4.7%) and thousand grain weight (177.0-374.9g). There were significant positive and negative associations among mineral elements and quality traits. The principal component analysis differentiated some maize landraces from the rest, and these diverse landraces could be used in the maize breeding program with biofortification purpose

Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.)

Lentil is the sixth most important pulse crop terms of production in the world, but the number of available and mapped SSR markers are limited. To develop SSR markers in lentil, four genomic libraries for (CA)n, (GA)n, (AAC)n and (ATG)n repeats were constructed. A total of 360 SSR primers were designed and validated using 15 Turkish lentil cultivars and genotypes. The most polymorphic repeat motifs were GA and CT, with a mean number of alleles per locus of 7.80 and 6.55, respectively. Seventy-eight SSR primers amplified a total of 400 polymorphic alleles, whereas 71 SSR primers produced markers within the expected size range. For 78 polymorphic SSR primers, the average number of alleles per locus was 5.1 and PIC value ranged from 0.07 to 0.89, with an average of 0.58. A linkage map was constructed using 92 individual F2 plants derived from a cross between Karacadağ × Silvan, with 47 SSR markers. The SSR markers developed in this study could be used for germplasm classification and identification and mapping of QTL in lentil.Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (TÜBİTAK)-TOVAG-104O186 Çukurova Üniversitesi BAP Birimi-ZF2004BAP1

Ipbs-retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Lack of requisite genetic variation in cultivated species has necessitated systematic collection, documentation and evaluation of wild Cicer species for use in chickpea variety improvement programs. Cicer arietinum has very narrow genetic variation, and the use of a wild relative in chickpea breeding could provide a good opportunity for increasing the available genetic variation of cultivated chickpea. Genetic diversity and the relationship of 71 accessions, from the core area of chickpea origin and domestication (Southeastern Turkey), belonging to five wild annual species and one cultivated species (Cicer arietinum) were analysed using iPBS-retrotransposon and ISSR markers. A total of 136 scorable bands were detected using 10 ISSR primers among 71 accessions belonging to 6 species, out of which 135 were polymorphic (99.3 %), with an average of 13.5 polymorphic fragments per primer, whereas iPBS detected 130 bands with 100 % polymorphism with an average of 13.0 bands per primer. C. echinospermum and C. pinnatifidum were the most diverse among species, whereas C. arietinum exhibited lower polymorphism. The average polymorphism information contents (PIC) value for both marker systems was 0.91. The clustering of the accessions and species within groups was almost similar, when iPBS and ISSR NeighborNet (NNet) planar graphs were compared. Further detailed studies are indispensable in order to collect Cicer germplasm, especially C. reticulatum, from southeastern Turkey particularly, from Karacadağ Mountain for preservation, management of this species, and to study their genetic diversity at molecular level. This study also demonstrates the utility and role of iPBSretrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in wild chickpea and in cultivated chickpea

Use of Genetic Engineering: Benefits and Health Concerns

WOS: 000467568700005

Variation for selected morphological and quality-related traits among 178 faba bean landraces collected from Turkey

WOS: 000342666200001Faba bean is cultivated worldwide and widely used in Mediterranean countries, Asia and Europe. However, only a few faba bean breeders are active in cultivar development. As a result, a limited number of varieties are available for growers. Plant genetic resources or germplasm are fundamental sources for plant breeding, and the assessment of the genetic diversity among germplasm accessions is useful to facilitate more efficient use of plant genetic resources. A mini-core collection of faba bean germplasm (178 landraces and four cultivars), from diverse geographic regions of Turkey, was assessed for agro-morphological performance and some quality traits. There were substantial variations for the investigated morphological and quality characteristics. The analysis of variance revealed that the differences among 182 accessions were significant for all the studied characters. Some accessions showed very good agronomic performance for some traits. Positive and negative correlations existed among different morphological and agronomic traits. Landraces have been classified into four different groups using a cluster analysis. These results suggest that an a priori classification of accessions according to the growing area does not strictly correspond to phenotypic grouping. From the spatial distribution of landraces, however, it has been possible to identify 'superior' accessions of some traits. These findings indicate a number of useful traits in the gene pools and a wide range of phenotypic variation that provides a good source of diversity for use in modern faba bean breeding programmes