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    Allelic diversity of a panel of Aegilops mutica Boiss (Amblyopyrym muticum (Boiss.) Eig) from Turkey
    (Cambridge Univ Press, 2022) Alsaleh, Ahmad; Cakir, Esra; Bektas, Harun; Ozkan, Hakan
    The members of the Aegilops genus serve as a vast pool of allele discovery for wheat improvement in abiotic and biotic stress responses. Aegilops mutica Boiss (Amblyopyrym muticum (Boiss) Eig) is an unexplored candidate with significant potential. Even though it has been used in cytogenetics applications within the last century, natural population diversity and allele discovery have been neglected. As an endemic species for Anatolia and the lower Caucasian region, it has an unexplored population structure. Here, seventy-five genotypes from five different newly collected populations from central Anatolia were evaluated with 29 polymorphic SSR loci. Significant diversity within (83%) and between (17%) the populations was obtained. Three of the populations were clearly separated, while two had some level of the mixture. Relatively easy cross-species hybridization and introgressions make Ae. mutica a good candidate for novel allele discovery and pre-breeding. Here, for the first time, representative natural populations of Ae. mutica were compared and population structures were revealed with SSR markers which may clear the misty vision that geneticists might have regarding Ae. mutica. This could be exploited in genetic resource conservation and breeding programs and maybe a point for further studies.
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    Dissection of quantitative trait loci for root characters and day length sensitivity in SynOpDH wheat (Triticum aestivum L.) bi-parental mapping population
    (Cambridge Univ Press, 2020) Bektas, Harun; Hohn, Christopher Earl; Waines, John Giles
    The genetics of the root system is still not dissected for wheat and lack of knowledge prohibits the use of marker-assisted selection in breeding. To understand the genetic mechanism of root development, Synthetic W7984 x Opata M85 doubled-haploid (SynOpDH) mapping population was evaluated for root and shoot characteristics in PVC tubes until maturity. Two major quantitative trait loci (QTLs) for total root biomass were detected on homoeologous chromosomes 2A and 2D with logarithm of the odds scores between 6.25-10.9 and 11.8-20.86, and total phenotypic effects between 12.7-17.7 and 26.6-40.04% in 2013 and 2014, respectively. There was a strong correlation between days to anthesis and root and shoot biomass accumulation (0.50-0.81). The QTL for biomass traits on chromosome 2D co-locates with QTL for days to anthesis. The effect of extended vegetative growth, caused by photoperiod sensitivity (Ppd) genes, on biomass accumulation was always hypothesized, this is the first study to genetically support this theory.
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    Genetic Mapping of Quantitative Trait Loci (QTLs) Associated with Seminal Root Angle and Number in Three Populations of Bread Wheat (Triticum aestivum L.) with Common Parents
    (Springer, 2020) Hohn, Christopher E.; Bektas, Harun
    Drought tolerance of plants is related to their root system architecture. The architecture of a mature plant root system is closely linked to seminal root growth at the seedling stage; hence, selection for root characteristics at the seedling stage may identify genotypes better suited for drought conditions. Here, the genetics of seminal root angle and number were investigated in three doubled haploid mapping populations of wheat. All populations showed significant phenotypic variation for both traits and each demonstrated transgressive segregation. In total, 34 genomic regions were associated with seminal root traits; however, most QTLs were variable from year to year and were population specific. Considering only the results consistent across both years of experiments, five QTLs for seminal root angle were identified on chromosomes 2DS, 5BS, 6AL, 7A, and 7BS, but only the 2DS QTL appeared in two of the three populations. For the seminal root number, one QTL was identified on 4BL. Correlation analyses for seminal root angle, number, and seed weight revealed interesting relationships to consider for future research. In one population, those interactions wrongfully identified QTLs for seed weight as QTLs for seminal root traits. Our findings demonstrate that seminal root angle and number are complex traits and despite high heritability, may be more difficult to unwind than previously proposed.
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    Genome-wide association analysis of coleoptile length and interaction with plant height in durum wheat
    (Wiley, 2024) Sesiz, Ugur; Alsaleh, Ahmad; Bektas, Harun; Topu, Mustafa; Ozkan, Hakan
    Genotypes with longer coleoptiles can be sown in deep soil layers to reach the underground moisture needed for germination in dry areas. Developing new varieties with longer coleoptiles and shorter plant heights would be novel for wheat breeding and production. In this study, coleoptile lengths of a panel of durum wheat (Triticum turgidum ssp. durum) genotypes were determined, and 14,255 DArTseq (SNP and Silico-DArT) markers were used to identify coleoptile length-associated markers by genome-wide association study (GWAS). A wide genetic variation was accounted for both coleoptile length and plant height. The genetic relationships between coleoptile length and plant height were evaluated using plant height values from five different environments. Two environmentally stable MTAs were identified, one for coleoptile length (QCol.su.4BS) and one for plant height (QPh.su.4BS). These MTAs were located on the short arm of chromosome 4B, with LOD scores up to 12.00 and 17.00, respectively. A relatively high LD (r2 = 0.71) was accounted for between QCol.su.4BS and QPh.su.4BS. The LD block intervals of the MTAs overlapped with some genes with roles in plant growth and development. The functions of plausible candidate genes tell us that QCol.su.4BS may be controlling coleoptile length, whereas QPh.su.4BS may be regulating plant height. The combination of the two loci would be desirable. In conclusion, this study sheds light on the genetic control of coleoptile length and its relationship with plant height in durum wheat. Cultivars with longer coleoptiles perform better at emergence and seedling establishment.A diverse durum wheat panel was studied using GWAS analysis to evaluate coleoptile length and plant height.Two significant and stable genomic regions were identified for coleoptile length and plant height.These regions might enhance coleoptile length while reducing plant height.
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    Genome-Wide Association Study of Root-Lesion Nematodes Pratylenchus Species and Crown Rot Fusarium culmorum in Bread Wheat
    (Mdpi, 2022) Sohail, Quahir; Erginbas-Orakci, Gul; Ozdemir, Fatih; Jighly, Abdulqader; Dreisigacker, Susanne; Bektas, Harun; Birisik, Nevzat
    Triticum aestivum L., also known as common wheat, is affected by many biotic stresses. Root diseases are the most difficult to tackle due to the complexity of phenotypic evaluation and the lack of resistant sources compared to other biotic stress factors. Soil-borne pathogens such as the root-lesion nematodes caused by the Pratylenchus species and crown rot caused by various Fusarium species are major wheat root diseases, causing substantial yield losses globally. A set of 189 advanced spring bread wheat lines obtained from the International Maize and Wheat Improvement Center (CIMMYT) were genotyped with 4056 single nucleotide polymorphisms (SNP) markers and screened for root-lesion nematodes and crown rot resistance. Population structure revealed that the genotypes could be divided into five subpopulations. Genome-Wide Association Studies were carried out for both resistances to Pratylenchus and Fusarium species. Based on our results, 11 different SNPs on chromosomes 1A, 1B, 2A, 3A, 4A, 5B, and 5D were significantly associated with root-lesion nematode resistance. Seven markers demonstrated association with P. neglectus, while the remaining four were linked to P. thornei resistance. In the case of crown rot, eight different markers on chromosomes 1A, 2B, 3A, 4B, 5B, and 7D were associated with Fusarium crown rot resistance. Identification and screening of root diseases is a challenging task; therefore, the newly identified resistant sources/genotypes could be exploited by breeders to be incorporated in breeding programs. The use of the identified markers in marker-assisted selection could enhance the selection process and cultivar development with root-lesion nematode and crown rot resistance.
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    Next-Generation-Sequencing-Based Simple Sequence Repeat (SSR) Marker Development and Linkage Mapping in Lentil (Lens culinaris L.)
    (Mdpi, 2023) Topu, Mustafa; Sesiz, Ugur; Bektas, Harun; Toklu, Faruk; Ozkan, Hakan
    Simple Summary Although lentil is not as popular as other legumes, it is a climate-resilient legume crop because of its high protein content, nitrogen fixation, and abiotic stress tolerance ability. Even though it can be grown on almost every continent and is distributed globally, the use of existing genetic diversity in marker-assisted selection is still limited. In this study, novel SSR markers needed in lentil were identified using a next-generation sequencing approach. In this study, we created a ready-to-use SSR library for genetic diversity studies and breeding and evaluated the effectiveness of the obtained SSR markers in a recombinant inbred line (RIL) population. Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype Karacadag resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs.
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    On the Possible Trade-Off between Shoot and Root Biomass in Wheat
    (Mdpi, 2023) Bektas, Harun; Hohn, Christopher E.; Lukaszewski, Adam J.; Waines, John Giles
    Numerous studies have shown that under a limited water supply, a larger root biomass is associated with an increased above-ground biomass. Root biomass, while genetically controlled, is also greatly affected by the environment with varying plasticity levels. In this context, understanding the relationship between the biomass of shoots and roots appears prudent. In this study, we analyze this relationship in a large dataset collected from multiple experiments conducted up to different growth stages in bread wheat (Triticum aestivum L.) and its wild relatives. Four bread wheat mapping populations as well as wild and domesticated members of the Triticeae tribe were evaluated for the root and shoot biomass allocation patterns. In the analyzed dataset the root and shoot biomasses were directly related to each other, and to the heading date, and the correlation values increased in proportion to the length of an experiment. On average, 84.1% of the observed variation was explained by a positive correlation between shoot and root biomass. Scatter plots generated from 6353 data points from numerous experiments with different wheats suggest that at some point, further increases in root biomass negatively impact the shoot biomass. Based on these results, a preliminary study with different water availability scenarios and growth conditions was designed with two cultivars, Pavon 76 and Yecora Rojo. The duration of drought and water level significantly affected the root/shoot biomass allocation patterns. However, the responses of the two cultivars were quite different, suggesting that the point of diminishing returns in increasing root biomass may be different for different wheats, reinforcing the need to breed wheats for specific environmental challenges.
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    Preliminary tests indicate the absence of polymorphism among 1RS.1BL translocations in wheat for root biomass enhancement
    (Springer, 2021) Hohn, Christopher E.; Bektas, Harun
    The introduction of the short arm of rye chromosome 1R (1RS) into wheat significantly increased grain yields. Studies have shown that 1RS carries a locus controlling root biomass and improves canopy water status under water-stressed conditions. The general genetic map location of the locus is known but allelic variation would facilitate precise mapping and identification of the responsible gene(s). To this end, six 1RS.1BL translocations from various sources in three wheat backgrounds were tested for root biomass and response to drought but no significant differences among different 1RS arms were observed. The behavior of the standard 1RS.1BL translocation in cv. Pavon 76 in various experiments suggested that wheat chromosome arm 1BS of Pavon 76 may carry a locus for root system plasticity. A set of single substitutions of chromosome 1B from 15 different sources, in the same genetic background of cv. Pavon 76, were tested for root biomass in various experiments. Again, no significant variation among the 1B substitution lines was observed. These results suggest that either no allelic variation at the targeted loci exists, or the sets of lines were biased. While various 1B chromosomes originated from a random sample of wheats, all 1RS arms were imported into wheat from various triticales, perhaps preselecting certain allelic combinations.
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    QTL mapping of seedling root traits in Synthetic W7984 x Opata M85 bread wheat (Triticum aestivum L.) mapping population
    (Tubitak Scientific & Technological Research Council Turkey, 2021) Bektas, Harun
    Root system architecture, as a complex trait, has gained attention due to climate change and abiotic stress pressure on crops. The incorporation of root traits in breeding objectives may enable new advances in climate-resilient crops. Here, the genetics of the seedling root system architecture in the Synthetic W7984 x Opata M85 Doubled Haploid mapping population was investigated. Three traits at the seedling stage and mature stage root and shoot biomass traits were mapped for quantitative trait loci (QTL) identification. A total of five different loci on chromosomes 1B, 5A, and 7D with major effects were identified for total root length, primary root length, and seminal root growth angle. Four regions on chromosomes 2A, 5A, and 7D had colocating loci for seedling and mature stage root traits. Chromosome 5A, with a locus affecting most of the seedling root traits, is promising. The correlations between seedling and mature root traits, and newly identified QTL for seedling root traits, maybe promising to unravel the genetic structure of root traits and for the marker-assisted selection.
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    Root system architecture and seed weight relations in forage pea (Pisum sativum ssp. arvense L. Poir.)
    (Univ Federal Santa Maria, 2022) Acikbas, Semih; Ozyazici, Mehmet Arif; Bektas, Harun
    Forage pea (Pisum sativum ssp. arvense (L.) Poir.) is an important legume crop for fresh and dry herbage production with high input costs as irrigation and fertilization. Selection and breeding of accessions for improved drought tolerance, water, and mineral uptake efficiency become a necessity, rather than a choice. This study evaluated a set of forage pea accessions for the seedling root system architecture diversity and seed reserve utilization, under controlled conditions. Eight cultivars and an elite breeding line were evaluated for the first time in a plexiglass system. The number and lengths of the roots in each depth zone (0, 5, 10, 15+ cm) were evaluated and significant diversity was identified. The cultivar Livioletta had the highest number of roots and total root length. There was a significant correlation between seed weight, seed reserve utilization ratio, and root system vigor. Accessions with the highest seed reserve utilization had the highest total root length and numbers. Seedling root system vigor seems to be effective in predicting the fate of the accessions through maturity. The results suggested a possibility of seedling root selection for forage crop breeding.
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    Root system variation of pulse crops at early vegetative stage
    (Univ Agr Sci & Veterinary Med Cluj-Napoca, 2020) Ceritoglu, Mustafa; Ceritoglu, Figen; Erman, Murat; Bektas, Harun
    Grain legumes known as Pulse crops are economically and nutritionally one of the most important crop families after cereals. Climate change and abiotic stress factors are limiting yield potential in these crops. Root system architecture, a neglected field, is promising for improved environmental adaptability and higher growth potential. Genotypes with deep and dense root system may cope better with water and nutrient limitations. This study aimed to evaluate 12 common cultivars from six different legume species. Root system architectures were evaluated under controlled conditions in a plexiglass system at the early vegetative stage. Roots were divided into four depth zones (0, 5, 10, 15> cm), and inter and intra species diversity were analysed. Significant diversity was obtained within and between the species. Bean, chickpea, and broad bean constituted deeper and dense root systems while lentil, soybean, and pea formed non-dense and shallower root systems. There was a significant correlation between earliness and early vegetative root vigour. The results of the study may provide a better understanding of the root system architectures of each species-genera. The results presented here may shed light on the selection of root traits in legume breeding programs.
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    Turkish durum wheat conserved ex-situ and in situ unveils a new hotspot of unexplored genetic diversity
    (Wiley, 2022) Alsaleh, Ahmad; Bektas, Harun; Baloch, Faheem Shehzad; Nadeem, Muhammad Azhar; Ozkan, Hakan
    Durum wheat (Triticum turgidum L.) is the 10(th) most cultivated crop and is a vital food source for human consumption. Genetic diversity in durum wheat is still an unexplored subject, and gene banks are filled with accessions waiting to be screened. Here, four different groups of durum wheat, Turkish and foreign cultivars, and in situ and ex situ landraces were evaluated for population structure and genetic diversity. A collection of 129 durum wheat accessions were genotyped, with a total of 6,357 markers (SilicoDArT, SNP [single-nucleotide polymorphism], and simple sequence repeats [SSRs]). The highest mean allele number per marker (1.562) was obtained with SNP markers in ex situ landraces; the lowest mean allele number per marker (0.788) was obtained with SSR markers in the foreign cultivars. The minimum percentage of polymorphic loci was 38.70% observed with SSR markers in foreign cultivars; the maximum was 76.20% in SilicoDArT markers in ex situ landraces. According to Neighbor-Joining analyses, the studied collection was divided into groups of cultivars and landraces, with some level of admixtures. Structure and principal coordinate analysis obtained distinct clusters for ex situ landraces and foreign cultivars, supported by Neighbor-Joining analysis. A significant level of intergroup and intragroup variation was observed, and Turkish ex situ landraces were found as the most diverse and distinct group in the collection. Turkish landraces may be a promising source of novel allelic diversity that can be used in durum wheat breeding worldwide.