First Report of Alternaria alternata Causing Leaf Spot Diseases of Cotton in Türkiye.

Cotton (Gossypium hirsutum L.) is a crucial crop for the textile industry. Sanliurfa is the major cotton production area in southeast Türkiye (USDA 2021). In the summers of 2021 and 2022, the mid to late season desiccation of leaves, stems and bolls as well as severe defoliation were observed in different cotton fields and cultivars in a 30-ha area centered around 36°51'15.7"N, 39°07'12.2"E. Approximately 45% of the plants were severely affected or completely desiccated. Initially, symptoms were circular, pinhead, necrotic lesions surrounded by a purple halo, scattered all around the infected leaves. As the disease progressed, it spread to bracts, petioles, stem and bolls. The necrotic lesions continued to expand, and formed irregular shapes by coalescing, occupied the whole tissue . Finally, severe infection resulted in premature defoliation. A secondary host (Prosopis farcta) of the inoculum of A. alternata is found in the field where the symptoms of pathogen was seen. The disease symptoms were similar to those described in cotton by Macauley (1982). Infected leaf samples with mycelia were collected (n=35) from 25 diseased plants. The samples derived from lesions on infected leaves were cut into 4- to 5- mm pieces, treated in 2% sodium hypochlorite, dipped in water, plated on potato dextrose agar (PDA) amended with 30 mg/L of streptomycin sulphate, and kept at 27°C in the dark. All the isolated fungal samples formed dark olive-green colonies. For morphological characterization, the colonies were examined under light microscopy at ×400 magnification. Conidia formed both cross or longitudinal septa, and were obclavate to elliptical and measured 16.2 to 30.5 µm long and 7.5 to 10.6 µm wide (n=14). The morphological characters were consistent with the genus Alternaria using a taxonomic key (Barnett and Hunter 1972). For pathogenicity test, healthy cotton plants were grown at 15 to 29°C in greenhouse. Conidial suspension (10 6 per mL) was sprayed on 30-d old plants (n=16) while control plants were sprayed with water. Then, the plants were covered with plastic bags (28x45 cm) at nights, opened in the morning. The disease symptoms were seen 20 days after artificial inoculation. However, the control group showed no symptoms. The pathogen was re-isolated from infected leaves. To confirm the result, the pathogenicity test was conducted twice. Then, DNA was extracted from conidia and mycelia using CTAB method with slight modification (Doyle and Doyle 1990). The nuclear rDNA internal transcribed spacer (ITS) and plasma membrane ATPase regions were (Lawrence et al. 2014; White et al. 1990) amplified, using primers ITS4/ITS5 and ATPDF1/ATPDR1, respectively. The PCR products were Sanger-sequenced and were uploaded to GenBank (accession nos. ITS: OP615138.1, ATPase: OP612816.1). The sequenced parts of the genes were 554 bp and 1025 bp, and showed 100% (ITS) and 97.99% (ATPase) nucleotide identity with the corresponding sequences (MT446176.1, ON442363.1) of the reference strains of A. alternata. To the best of our knowledge, this is the first report of A. alternata causing leaf blight of cotton in Türkiye. In several cotton-growing regions, A. alternata leaf spot epidemics have caused yield loss from 25% (Israel) to 37% (India) (Padaganur et al. 1989; Rotem et al. 1988). Although yield loss caused by the pathogen depends on environmental conditions, observations in Türkiye cotton fields suggest A. alternata has the potential to cause yield loss up to 30% under severe infection.

Mapping QTLs for Super-Earliness and Agro-Morphological Traits in RILs Population Derived from Interspecific Crosses between Pisum sativum × P. fulvum.

Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing season and may also expand arable lands to meet global food demands. The primary objective of the present study was to investigate quantitative trait loci (QTLs) for super-earliness and important agro-morphological traits in a recombinant inbred line (RIL) population derived from an interspecific cross. A population of 114 RILs developed through single-seed descent from an interspecific cross involving Pisum sativum L. and P. fulvum Sibth. et Sm. was evaluated to identify QTLs for super-earliness and important agro-morphological traits. A genetic map was constructed with 44 SSRs markers representing seven chromosomes with a total length of 262.6 cM. Of the 14 QTLs identified, two were for super-earliness on LG2, one for plant height on LG3, six for number of pods per plant on LG2, LG4, LG5 and LG6, one for number of seeds per pod on LG6, one for pod length on LG4 and three for harvest index on LG3, LG5, and LG6. AA205 and AA372-1 flanking markers for super-earliness QTLs were suggested for marker-assisted selection (MAS) in pea breeding programs due to high heritability of the trait. This is the first study to map QTLs originating from P. sativum and P. fulvum recently identified species with super-earliness character and the markers (AA205 and AA372-1) linked to QTLs were valuable molecular tools for pea breeding.

Inheritance of androgenesis response in pepper.

BACKGROUND: Anther culture has become an important part of pepper breeding. Response to haploidy via androgenesis is highly genotype-specific. However, studies on the inheritance of response to anther culture are lacking. Therefore, the study aimed to determine the inheritance of androgenesis. METHODS AND RESULTS: The plant material included crosses involving Capsicum annuum L. (253 A, and Inan3363) X C. chinense PI 159,236 populations. To estimate the heritability of the trait, two pepper lines with very high androgenesis responses were crossed with PI 159,236, a non-responsive accession. The androgenesis response was phenotyped using the parents, F1, F2, BC1P1, and BC1P2/P3 created through reciprocal crosses. Using variance components, the number of genes controlling the trait, broad (H2 = 0.97), and narrow sense heritabilities (h2 = 0.20), genetic variance (VG=113.8), the additive (VA=23.9), and the dominance gene variances (VD = 89.9), as well as the environmental variance (VE = 3.6) were calculated. Additive and dominant gene effects were 21% and 79%, respectively. Results derived from two different populations showed that the number of genes controlling the trait was between 1.96 and 2.46, and H2 = 0.96-0.97, h2 = 0.20-0.65, VG=91.8-113.8, VA, = 23.9-62.7, VD = 29.1-89.9, and VE=3.5-3.6 were calculated. The X2 analysis indicated that the most suitable one is the 9: 3: 4 epistatic genetic model (X2 = 2.13, P = 0.343, N = 155). CONCLUSIONS: Results obtained from two different populations indicate the existence of a few major genes for response to androgenesis in pepper. Elucidating the inheritance of androgenesis is expected to pave the way for tagging the gene(s) in the pepper genome.

Development of molecular markers linked to QTL/genes controlling Zn efficiency.

BACKGROUND: Zinc (Zn) deficiency is a widespread problem in reducing the yield and quality of crop plants worldwide. It is important to utilize molecular markers linked to Zn efficiency to develop high Zn efficient cultivars in pepper (Capsicum annuum L.). METHODS AND RESULTS: In present study, genetic map was constructed using a F2 populations derived from C. annuum L. (Alata 21A) × C. frutescens L. (PI 281420) cross. The quantitative trait locus (QTLs) for Zn efficiency were mapped using F2:3 population. A genetic map with 929.6 cM in length and 12 linkage groups were obtained using 62 markers (31 sequence-related amplified polymorphism (SRAP), 19 simple sequence repeat (SSR) and 11 random amplified polymorphic DNA (RAPD) markers). The 41 linked QTLs related with nine (9) Zn efficiency characters were mapped on linkage groups. Results suggest that selecting plants for tolerance to Zn deficiency are expected to be rather responsive among segregating populations for breeding and developing Zn efficient genotypes in pepper. CONCLUSIONS: The molecular markers are expected to aid selection and expedite breeding peppers resistant to Zn deficiency in soils low for available Zn contents.

Enhancing soybean photosynthetic CO2 assimilation using a cyanobacterial membrane protein, ictB.

Soybean C3 photosynthesis can suffer a severe loss in efficiency due to photorespiration and the lack of a carbon concentrating mechanism (CCM) such as those present in other plant species or cyanobacteria. Transgenic soybean (Glycine max cv. Thorne) plants constitutively expressing cyanobacterial ictB (inorganic carbon transporter B) gene were generated using Agrobacterium-mediated transformation. Although more recent data suggest that ictB does not actively transport HCO3-/CO2, there is nevertheless mounting evidence that transformation with this gene can increase higher plant photosynthesis. The hypothesis that expression of the ictB gene would improve photosynthesis, biomass production and seed yield in soybean was tested, in two independent replicated greenhouse and field trials. Results showed significant increases in photosynthetic CO2 uptake (Anet) and dry mass in transgenic relative to wild type (WT) control plants in both the greenhouse and field trials. Transgenic plants also showed increased photosynthetic rates and biomass production during a drought mimic study. The findings presented herein demonstrate that ictB, as a single-gene, contributes to enhancement in various yield parameters in a major commodity crop and point to the significant role that biotechnological approaches to increasing photosynthetic efficiency can play in helping to meet increased global demands for food.

Development of co-dominant SCAR markers linked to resistant gene against the Fusarium oxysporum f. sp. radicis-lycopersici.

We developed highly reliable co-dominant SCAR markers linked to the Frl gene. FORL testing is difficult. The marker is expected to be quickly adapted for MAS by tomato breeders. Fusarium oxysporum f. sp. radicis-lycopersici causes Fusarium crown and root rot (FCR), an economically important soil-borne disease of tomato. The resistance against FCR is conferred by a single dominant gene (Frl) located on chromosome 9. The aim of this study was to develop molecular markers linked to the Frl gene for use in marker-assisted breeding (MAS) programs. The FCR-resistant 'Fla. 7781' and susceptible 'B560' lines were crossed, and F1 was both selfed and backcrossed to 'B560' to generate segregating F2 and BC1 populations. The two conserved set II (COSII) markers were found linked to the Frl gene, one co-segregated with FCR resistance in both F2 and BC1 populations and the other was 8.5 cM away. Both COSII markers were converted into co-dominant SCAR markers. SCARFrl marker produced a 950 and a 1000 bp fragments for resistant and susceptible alleles, respectively. The linkage of SCARFrl marker was confirmed in BC2F3 populations developed by backcrossing the resistant 'Fla. 7781' to five different susceptible lines. The SCARFrl marker has been in use in the tomato breeding programs in BATEM, Antalya, Turkey, since 2012 and has proved highly reliable. The SCARFrl marker is expected to aid in the development of FCR-resistant lines via marker-assisted selection (MAS).

Elucidating genetic relationships, diversity and population structure among the Turkish female figs.

A collection of 96 female Turkish fig (Ficus carica L.) accessions was studied to elucidate genetic structure and estimate diversity and genetic similarity distribution among the female figs present in Turkish genetic resources, using 157 molecular genome markers including 129 sequence-related amplified polymorphisms, 21 random amplified polymorphic DNAs, and 7 simple-sequence repeats. The plant samples mainly included Turkish fig collections selected throughout the country over the course of a half-century. Neighbor-joining analysis revealed continuous dissimilarity range, and it was difficult to classify figs into distinct groups. The principle component analysis produced similar results. The analysis of molecular variance indicated that 95 and 93% of genetic variation were explained by within geographic origins and similar fruit rind color, respectively. Sub-structuring Bayesian analysis assigned the 96 female figs into four sub-populations, and indicated that they were highly related. The corrected allelic pairwise distances among the six geographic origins were less than 5%. This study suggests that geography- and color-based groups were not genetically distinct among the Turkish figs.

Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

Development of SRAP, SRAP-RGA, RAPD and SCAR markers linked with a Fusarium wilt resistance gene in eggplant.

Fusarium wilt (Fusarium oxysporum Schlecht. f. sp. melongenae) is a vascular disease of eggplant (Solanum melongena L.). The objectives of this work were (1) to confirm the monogenic inheritance of fusarium wilt resistance in eggplant, (2) to identify molecular markers linked to this resistance, and (3) to develop SCAR markers from most informative markers. We report the tagging of the gene for resistance to fusarium wilt (FOM) in eggplant using SRAP, RGA, SRAP-RGA and RAPD markers. Analysis of segregation data confirmed the monogenic inheritance of resistance. DNA from F(2) and BC(1) populations of eggplant segregating for fusarium wilt resistance was screened with 2,316 primer combinations to detect polymorphism. Three markers were linked within 2.6 cM of the gene. The codominant SRAP marker Me8/Em5 and dominant SRAP-RGA marker Em12/GLPL2 were tightly linked to each other and mapped 1.2 cM from the resistance gene, whereas RAPD marker H12 mapped 2.6 cM from the gene and on the same side as the other two markers. The SRAP marker was converted into two dominant SCAR markers that were confirmed to be linked to the resistance gene in the F(2,) BC(1) and F(2) of BC(3) generations of the same cross. These markers provide a starting point for mapping the eggplant FOM resistance gene in eggplant and for exploring the synteny between solanaceous crops for fusarium wilt resistance genes. The SCAR markers will be useful for identifying fusarium wilt-resistant genotypes in marker-assisted selection breeding programs using segregating progenies of the resistant eggplant progenitor used in this study.

Dicamba resistance: enlarging and preserving biotechnology-based weed management strategies.

The advent of biotechnology-derived, herbicide-resistant crops has revolutionized farming practices in many countries. Facile, highly effective, environmentally sound, and profitable weed control methods have been rapidly adopted by crop producers who value the benefits associated with biotechnology-derived weed management traits. But a rapid rise in the populations of several troublesome weeds that are tolerant or resistant to herbicides currently used in conjunction with herbicide-resistant crops may signify that the useful lifetime of these economically important weed management traits will be cut short. We describe the development of soybean and other broadleaf plant species resistant to dicamba, a widely used, inexpensive, and environmentally safe herbicide. The dicamba resistance technology will augment current herbicide resistance technologies and extend their effective lifetime. Attributes of both nuclear- and chloroplast-encoded dicamba resistance genes that affect the potency and expected durability of the herbicide resistance trait are examined.