Drought Responsive Putative Marker-Trait Association in Tall Fescue as Influenced by the Presence of a Novel Endophyte

Tall fescue (Festuca arundinacea Schreb.) is one of the most important cool-season perennial obligatory outcrossing forage grasses in the United States. The production and persistence of tall fescue is significantly affected by drought in the south-central United States. Shoot-specific endophyte (Epichloë coenophiala)-infected tall fescue showed superior performance under both biotic and abiotic stress conditions. We performed a genome-wide association analysis using clonal pairs of novel endophyte AR584-positive (EP) and endophyte-free (EF) tall fescue populations consisting of 205 genotypes to identify marker-trait associations (MTAs) that contribute to drought tolerance. The experiment was performed through November 2014 to June 2018 in the field, and phenotypic data were taken on plant height, plant spread, plant vigor, and dry biomass weight under natural summer conditions of sporadic drought. Genotyping-by-sequencing of the population generated 3,597 high quality single nucleotide polymorphisms (SNPs) for further analysis. We identified 26 putative drought responsive MTAs (17 specific to EP, eight specific to EF, and one in both EP and EF populations) and nine of them (i.e., V.ep_10, S.ef_12, V.ep_27, HSV.ef_31, S.ep_30, SV.ef_32, V.ep_68, V.ef_56, and H.ef_57) were identified within 0.5 Mb region in the tall fescue genome (44.5-44.7, 75.3-75.8, 77.5-77.9 and 143.7-144.2 Mb). Using 26 MTAs, 11 tall fescue genotypes were selected for subsequent study to develop EP and EF drought tolerant tall fescue populations. Ten orthologous genes (six for EP and four for EF population) were identified in Brachypodium genome as potential candidates for drought tolerance in tall fescue, which were also earlier reported for their involvement in abiotic stress tolerance. The MTAs and candidate genes identified in this study will be useful for marker-assisted selection in improving drought tolerance of tall fescue as well opening avenue for further drought study in tall fescue.

Mapping QTL for summer dormancy related traits in tall fescue (Festuca arundinacea Schreb.)

Summer dormancy is an important stress avoidance mechanism of cool season perennial grasses to persist well under harsh summer conditions. QTL associated with summer-dormancy related traits in tall fescue has significant breeding implications. An F1 pseudo testcross population was developed by crossing a Mediterranean (103-2) to a Continental parent (R43-64). The population was genotyped using 2,000 SSR and DArT markers. Phenotyping was done in growth chambers and in two Oklahoma, USA locations. Total length of R43-64 and 103-2 maps were 1,956 cM and 1,535 cM, respectively. Seventy-seven QTL were identified in the male and 46 in the female parent maps. The phenotypic variability explained by the QTL ranged between 9.91 and 32.67%. Among all the QTL, five summer dormancy related putative QTL were identified in R43-64 linkage groups (LGs) 4, 5, 12, 20 and 22 and two in 103-2 LGs 5 and 17. All the putative summer dormant QTL regions in male map showed pleiotropic responses and epistatic interactions with other summer dormant and stress responsive QTL regions for plant height, new leaf and dry biomass weight. The flanking markers related to the QTL reported in this study will be useful to improve tall fescue persistence in dry areas through marker-assisted breeding.

Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces

BACKGROUND

In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB).

RESULTS

A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms.

CONCLUSION

Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.

Prevalence and Predictors of Depression among Patients with Type 2 Diabetes: A Multicenter Cross-sectional Study from Bangladesh

Depression is a common comorbidity of type 2 diabetes mellitus (T2DM) which adversely affects diabetes management and outcome. Identifying and treating comorbid depression may improve diabetes care. This cross-sectional study was conducted in several tertiary hospitals throughout Bangladesh from July 2017 to April 2018. Nine hundred (900) adult patients with T2DM aging ≥25 years having diabetes for at least 6 months and equal numbers of non-diabetic otherwise healthy controls were recruited from the outpatient departments of these centers. Depression was assessed in all consenting patients and controls by administering the Bangla (local language) version of the PRIME-MD Patient Health Questionnaire (PHQ-9); participants obtaining a score of 5 or more were labeled to have depression. Depression was present in 60.3% of T2DM patients and in 29.4% of controls. Statistically significant difference was found in age, marital status, occupation, body mass index (BMI), waist circumference, systolic blood pressure (BP), diastolic BP and PHQ-9 score between diabetic and non-diabetic subjects (<0.001). T2DM subjects had 4.71-fold higher odds of depression in comparison to the controls (95% CI: 3.76-5.90; p<0.001). Age ≥50 years, unmarried status, years of schooling ≤10 years, underweight, abdominal obesity, and hypertension appeared to be the significant predictors of depression in the study subjects. In T2DM subjects, diabetes in the family members, the presence of other comorbidities, diabetic complications, diabetes duration >5 years, insulin use, using insulin syringe for injection, albuminuria and CKD were the important predictors of depression. Our study found higher prevalence and risk of depression in T2DM patients than their non-diabetic counterparts. T2DM patients should be screened for depression in order to achieve and maintain the treatment goals.

Expression of a rice soluble starch synthase gene in transgenic wheat improves the grain yield under heat stress conditions

Wheat (Triticum aestivum L.) is a temperate cereal with an optimum temperature range of 15-22°C during the grain filling stage. Heat stress is one of the major environmental constraints for wheat production worldwide. Temperatures above 25°C during the grain filling stage significantly reduced wheat yield and quality. This reduction was reported due to the inactivation of the soluble starch synthase, a key heat-labile enzyme in starch transformation of wheat endosperm. To improve wheat productivity under heat stress, the rice soluble starch synthase I, under the control of either a constitutive promoter or an endosperm-specific promoter, was expressed in wheat and the transgenic lines were monitored for expression and the effects on yield-related traits. The results showed that the transgenic wheat events expressed rice soluble starch synthase I at a high level after four generations, and transgenic plants produced grains of greater weight during heat stress. Under heat stress conditions, the thousand kernel weight increased 21-34% in T2 and T3 transgenic plants compared to the non-transgenic control plants. In addition, the photosynthetic duration of transgenic wheat was longer than in non-transgenic controls. This study demonstrated that the engineering of a heat tolerant soluble starch synthase gene can be a potential strategy to improve wheat yield under heat stress conditions.

Molecular discrimination of tall fescue morphotypes in association with Festuca relatives

Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute's core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. F. pratensis and F. arundinacea var. glaucescens, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and F. mairei (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both F. pratensis and F. mairei formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity.

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.

De Novo Assembly and Characterization of Tall Fescue Transcriptome under Water Stress

Water stress is a fundamental problem for tall fescue [Lolium arundinaceum (Schreb.) Darbysh.] cultivation in the south-central United States. Genetic improvement of tall fescue for water-stress tolerance is the key strategy for improving its persistence in the region. Genotypes with contrasting characteristics for relative water content and osmotic potential were identified from a tall fescue population. Transcriptome profiling between water-stress-tolerant (B400) and water-stress-susceptible (W279) genotypes was performed to unravel the genetic regulatory mechanism of water-stress responses in tall fescue. RNA samples from leaf, shoot, root, and inflorescence were pooled and sequenced through Illumina paired-end sequencing. A total of 199,399 contigs were assembled with an average length of 585 bp. Between the two genotypes, 2986 reference transcripts (RTs) were significantly differentially expressed and 1048 of them could be annotated and found to associate with metabolic pathways and enzyme coding genes. In total, 175 differentially expressed RTs were reported for various stress-related functions. Among those, 65 encoded kinase proteins, 40 each encoded transposons, and transporter proteins were previously reported to be involved with abiotic stress responses. A total of 6348 simple sequence repeats and 6658 single-nucleotide polymorphisms were identified in the contig sequences. Primers were developed from the corresponding sequences, which might be used as candidate gene markers in tall fescue. This study will lead to identification of genes or transcription factors related to water-stress tolerance and development of a comprehensive molecular marker system to facilitate marker-assisted breeding in tall fescue.