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

Diversity Assessment of Turkish Maize Landraces Based on Fluorescent Labelled SSR Markers

Landraces of maize represent a valuable genetic resource for breeding and genetic studies. Since 1970, landraces have been collected from all over Turkey, but the genetic diversity represented in this collection is still largely unknown. In this study, a sample of 98 landraces sampled from 45 provinces of Turkey was assessed genotypically at 28 simple sequence repeat (SSR) loci and phenotypically for 19 morphological traits. The landraces varied significantly for all the latter traits. A total of 172 SSR alleles were detected, giving a mean of 6.21 alleles per locus. The genetic distance between pairs of landraces ranged from 0.18 to 0.63, with a mean of 0.35. Positive and negative correlation exists among different morphological and agronomic traits. Positive association among different traits showed that improvement of one character may simultaneously improve the other desired trait. Based on UPGMA dendrogram and Neighbor-Net (NNET) analyses from both morphological traits and SSR data, respectively, it is obvious that maize landraces from the same geographical region were often placed in different clusters, indicating that grouping based on genetic parameters was not closely related to the geographic origin. The wide diversity present in Turkish maize landraces could be used as genetic resource in designing maize breeding program for developing new cultivars adapted to different geographic and climatic conditions, and may also contribute to worldwide breeding programs. © 2011 Springer-Verlag.Firat University Scientific Research Projects Management Unit: ZF2004BAP17 TOVAG-104O186Acknowledgement We thank the Menemen gene bank (Aegean Agricultural Research Institute, Izmir, Turkey) for the kind provision of landrace seed stocks. The authors express their gratitude to TÜBİTAK (The Scientific and Technological Research Council of Turkey, TOVAG-104O186) and University of Cukurova, Scientific Research Projects Unit (ZF2004BAP17) for their financial support

Effect of salinity stress on dry matter production and ion accumulation in hybrid maize varieties

The salt stress tolerance of 19 hybrid maize (Zea mays L.) varieties was tested in nutrient solution during the early growth stage under controlled environmental conditions. For the salt stress treatment, sodium chloride (NaCl) was applied to nutrient solution at a concentration of 250 mM for 6 days before the harvest. Plants were harvested after 17 days of growth and analyzed for shoot and root dry matter production, severity of leaf damage (necrotic patches on older leaves), and the concentrations of potassium (K), sodium (Na) and calcium (Ca) in the roots and shoots. The varieties differed greatly in their response to the NaCl treatment. The development time and severity of leaf symptoms caused by 250 mM NaCl were varied markedly among the varieties. Based on the severity of leaf symptoms, the varieties Maverik and C.7993 were classified as the most tolerant and sensitive varieties, respectively. The decreases in the shoot dry matter production as a consequence of the NaCl treatment were higher than the decreases in root growth. There was also a marked genotypic variation in concentrations of K, Ca and Na in roots and particularly in shoots. The higher salt tolerance in maize varieties based on the severity of leaf symptoms was associated with significantly lower Na concentrations in shoots. The K/ Na and Ca/Na ratios were significantly greater in most of the tolerant varieties. The most sensitive variety, C.7993, contained a 4-fold greater Na concentration in shoots than the most tolerant variety, Maverik. The varieties RX.9292 and MF.714 also contained very high Na in shoots and showed severe toxicity symptoms on leaves. Besides Maverik, P.3394 and P.3223, with their low shoot Na concentrations, could also be considered tolerant varieties. Under salt treatment significant correlations were found between K/Na ratios and shoot dry matter production (r = 0.541***), K/Na ratios and leaf damage (r = -0.411***), and Ca/Na ratios and shoot dry matter production (r = 0.444***). The results indicate the existence of a large genotypic variation in tolerance to NaCl toxicity in maize that should be exploited in breeding programs aiming to develop maize varieties with high NaCl tolerance during the early growth stages. Among the ions measured, shoot Na concentration was a reliable screening parameter in ranking varieties for their tolerance to salt stress. © TÜBİTAK

Development of end-stage renal disease at a young age in two cases with joubert syndrome

PubMedID: 25818971Joubert syndrome (JS) is an autosomal recessive genetic disorder. To date, mutations in 20 genes of the genetically heterogeneous JS and JS-related disorders (JSRD) have been reported. Renal involvement occurs in 2-20% of JS cases. Identified renal abnormalities are cystic dysplasia and nephronophthisis. Here we report the clinical course and management of renal failure in early childhood. We present two cases diagnosed with JS that developed end-stage renal disease at young ages. In the genetic studies, a c.5668G>T (p.G1890*) homozygous stop mutation was identified in the CEP290 gene of one of the patients and a c.1303C>G (p.R435G) homozygous mutation in the INPP5E gene of the other. It has been emphasized that it is important to evaluate patients in terms of renal disease when monitoring the progress of Joubert syndrome, a condition that predominantly causes mental and motor development retardation. © 2014, Turkish Journal of Pediatrics. All rights reserved

Clinical, radiological, and genetic survey of patients with muscle-eye-brain disease caused by mutations in POMGNT1

PubMedID: 24731844Background To evaluate clinical, genetic, and radiologic features of our patients with muscle-eye-brain disease. Methods The data of patients who were diagnosed with muscle-eye-brain disease from a cohort of patients with congenital muscular dystrophy in the Division of Pediatric Neurology of Dokuz Eylül University School of Medicine and Gaziantep Children's Hospital between 2005 and 2013 were analyzed retrospectively. Results From a cohort of 34 patients with congenital muscular dystrophy, 12 patients from 10 families were diagnosed with muscle-eye-brain disease. The mean age of the patients was 9 ± 5.5 years (2-19 years). Mean serum creatine kinase value was 2485.80 ± 1308.54 IU/L (700-4267 IU/L). All patients presented with muscular hypotonia at birth followed by varying degrees of spasticity and exaggerated deep tendon reflexes in later stages of life. Three patients were able to walk. The most common ophthalmologic and radiologic abnormalities were cataracts, retinal detachment, periventricular white matter abnormalities, ventriculomegaly, pontocerebellar hypoplasia, and multiple cerebellar cysts. All of the patients had mutations in the POMGNT1 gene. The most common mutation detected in 66% of patients was c.1814 G > A (p.R605H). Two novel mutations were identified. Conclusions We suggest that muscle-eye-brain disease is a relatively common muscular dystrophy in Turkey. It should be suspected in patients with muscular hypotonia, increased creatine kinase, and structural eye and brain abnormalities. The c.1814 G > A mutation in exon 21 of the POMGNT1 gene is apparently a common mutation in the Turkish population. Individuals with this mutation show classical features of muscle-eye-brain disease, but others may exhibit a milder phenotype and retain the ability to walk independently. Congenital muscular dystrophy patients from Turkey carrying the clinical and radiologic features of muscle-eye-brain disease should be evaluated for mutations in POMGNT1 gene. © 2014 Elsevier Inc. All rights reserved

Identification of chromosomal regions in the genetic control of quality traits in durum wheat (Triticum Turgidum L.) from the fertile crescent

Durum wheat genetic resources from Turkey and Syria are expected to harbor novel alleles for most traits that are of interest to breeders and consumers. However, there have not been sufficient efforts to investigate the genetic structure of this gene pool. In this study, cultivar Kunduru-1149 (selected from one of the unique landraces, Kunduru) from Anatolia was crossed with a Syrian cultivar, Cham1, to produce recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. The RIL population was genotyped with simple sequence repeats, amplified fragment length polymorphism, and seed storage protein markers and analyzed for 9 different important quality traits of durum wheat in 8 different environments in Turkey, Syria, and Lebanon. We identified 59 QTLs of various quality and rheology traits using single-marker analysis. Some of the QTLs were also reported in earlier studies; however, new major QTLs were also identified in our QTL mapping population. In future studies, after validation, the markers linked with these QTLs can be used in marker-assisted durum wheat breeding. © TÜBİTAK

Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species

Even though lentil has been an important food legume for centuries, genetic studies in lentil are still in their infancy. Genetic diversity and relationships among wild Lens species from Turkey has seldom been investigated. Additionally, a limited number of simple sequence repeat (SSR) markers have been developed for use in breeding and genetic studies of lentil crop. In this study, molecular characterization of 50 accessions mostly from Turkey, belonging to 6 wild and 1 cultivated Lens species, was performed using newly developed inter-primer binding site (iPBS) retrotransposons and inter-SSR (ISSR) markers. The 10 iPBS primers generated a total of 151 scorable bands, of which 150 were polymorphic (99.3%) with an average of 15.0 polymorphic fragments per primer. The 10 ISSR primers detected 138 scorable bands showing 100% polymorphism, with an average of 13.5 bands per primer. The average polymorphism information content (PIC) value for ISSR markers (0.97) was higher than that for iPBS markers (0.90). Lens orientalis was found to be the most diverse species, raising the possibility of wide crosses with cultivated species Lens culinaris. Cultivated varieties also showed high level of polymorphism, at 82.92% and 51.92% with ISSR and iPBS markers, respectively. Lens lamottei and Lens tomentosus were found as the least polymorphic species using both marker systems. The grouping of accessions and species within clusters were almost similar when iPBS and ISSR graphs were compared. Our data also suggested the role of iPBS-retrotransposons as '. a universal marker' for molecular characterization of wild and cultivated Lens species. © 2014 Elsevier Ltd.Firat University Scientific Research Projects Management Unit: ZF2011YL1The authors express their gratitude to the University of Çukurova, Scientific Research Projects Unit ( ZF2011YL1 ) for financial support. Appendix

Magnesium- a Forgotten Element: Phenotypic Variation and Genome Wide Association Study in Turkish Common Bean Germplasm

Magnesium (Mg) is the fourth most abundant element in the human body and plays the role of cofactor for more than 300 enzymatic reactions. In plants, Mg is involved in various key physiological and biochemical processes like growth, development, photophosphorylation, chlorophyll formation, protein synthesis, and resistance to biotic and abiotic stresses. Keeping in view the importance of this element, the present investigation aimed to explore the Mg contents diversity in the seeds of Turkish common bean germplasm and to identify the genomic regions associated with this element. A total of 183 common bean accessions collected from 19 provinces of Turkey were used as plant material. Field experiments were conducted according to an augmented block design during 2018 in two provinces of Turkey, and six commercial cultivars were used as a control group. Analysis of variance depicted that Mg concentration among common bean accessions was statistically significant (p < 0.05) within each environment, however genotype × environment interaction was non-significant. A moderate level (0.60) of heritability was found in this study. Overall mean Mg contents for both environments varied from 0.33 for Nigde-Dermasyon to 1.52 mg kg−1 for Nigde-Derinkuyu landraces, while gross mean Mg contents were 0.92 mg kg−1. At the province level, landraces from Bolu were rich while the landraces from Bitlis were poor in seed Mg contents respectively. The cluster constellation plot divided the studied germplasm into two populations on the basis of their Mg contents. Marker-trait association was performed using a mixed linear model (Q + K) with a total of 7,900 DArTseq markers. A total of six markers present on various chromosomes (two at Pv01, and one marker at each chromosome i.e., Pv03, Pv07, Pv08, Pv11) showed statistically significant association for seed Mg contents. Among these identified markers, the DArT-3367607 marker present on chromosome Pv03 contributed to maximum phenotypic variation (7.5%). Additionally, this marker was found within a narrow region of previously reported markers. We are confident that the results of this study will contribute significantly to start common bean breeding activities using marker assisted selection regarding improved Mg contents