Genomic tools in pearl millet breeding for drought tolerance:Status and prospects

Pearl millet (Penisetum glaucum (L) R. Br.) is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by hundreds of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production

Comparative Transcriptome Analysis Reveals Genetic Mechanisms of Sugarcane Aphid Resistance in Grain Sorghum

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene clusters had differential expression during SCA infestation. Gene ontology enrichment and cluster analysis of genes differentially expressed after SCA infestation revealed consistent upregulation of genes controlling protein and lipid binding, cellular catabolic processes, transcription initiation, and autophagy in the resistant genotype. Genes regulating responses to external stimuli and stress, cell communication, and transferase activities, were all upregulated in later stages of infestation. On the other hand, expression of genes controlling cell cycle and nuclear division were reduced after SCA infestation in the resistant genotype. These results indicate that different classes of genes, including stress response genes and transcription factors, are responsible for countering the physiological effects of SCA infestation in resistant sorghum plants

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Citation: Serba, D. D., Uppalapati, S. R., Krom, N., Mukherjee, S., Tang, Y. H., Mysore, K. S., & Saha, M. C. (2016). Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. Bmc Genomics, 17, 14. doi:10.1186/s12864-016-3377-8Background: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1. 1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At >= 100x coverage and >= 5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions: The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion

Real-time Visual-Inertial Odometry for Event Cameras using Keyframe-based Nonlinear Optimization

Polymorphic conserved simple sequence repeats (SSR) markers detected among the two lowland and an upland genotypes. (DOCX 15 kb

Hybrid Bermudagrass Responses to Impaired Water Sources

Low-quality (i.e., impaired) water sources are commonly used to irrigate warm-season turfgrass landscapes as a result of limited supplies of potable water sources. Currently, there is great need to define the impacts of impaired water sources on turfgrass water consumption, growth, and quality. The objectives of this study were to characterize actual evaporation (ETa), clipping production, and quality of three hybrid bermudagrass varieties [‘TifTuf’, ‘Tifway’, and ‘Midiron’; Cynodon dactylon (L.) Pers. × C. traansvalensis Burtt Davy] grown under three water sources [reverse osmosis (RO), local well, and recycled], each supplied at full irrigation levels (1.0 × ETa) over two 8-week study periods. When pooling across water source and date, TifTuf maintained the highest visual quality and normalized difference vegetation index (NDVI) compared with both Midiron and Tifway. This was accompanied by a greater daily ETa rate, clipping production, and water use efficiency (WUE) compared with Midiron in both studies. When pooling across variety and date, daily ETa of turfgrass receiving recycled water was 5% to 10% less than those receiving the local well or RO water. In addition, turfgrasses receiving local well water held the greatest visual quality and NDVI compared with those receiving either RO water in the summer study. Visual quality and NDVI were also less in turfgrasses receiving RO water compared with those receiving local well or recycled water in the fall. Despite turfgrasses having a lower ETa under recycled water in both study periods, these plants had significantly greater clipping production compared with RO water in the summer. Also, clipping production under recycled water did not differ significantly from the other two sources in the fall study. Furthermoe, in both studies, WUE was similar for turfgrasses receiving recycled water compared with those receiving RO or local well water. Results demonstrated that irrigation water quality influences critical factors for hybrid bermudagrass growth and that considerable variability exists among three commercially available varieties for evapotranspiration rates, quality, and clipping production

Buffalograss genetic linkage mapping, chinch bug resistance characteristics and turfgrass performance

Buffalograss (Buchloe dactyloides (Nutt.) Engelm.) is a warm season perennial grass that has emerged as a turfgrass species due to its low maintenance requirements, and suitability for different turf uses. Turfgrass quality and western chinch bug (Blissus occiduus Barber) resistance are of interest to buffalograss breeding programs. The objectives of the current research were to (1) explore genetic variability for chinch bug resistance among available genotypes; (2) assess the merits of hybridization breeding in creating chinch bug resistance, buffalograss morphological traits, and turfgrass performance genetic variability; and (3) construct a genetic linkage map of diploid buffalograss. Fifteen buffalograss genotypes comprising diploids, tetraploids, pentaploid and hexaploids were evaluated for chinch bug resistance. Three half-sib populations were generated by crossing four diploid buffalograss genotypes (three females and one male). Random samples of the half- sibs were field evaluated for turfgrass performance. One full-sib population was selected, and 94 progeny from this population were evaluated for chinch bug resistance and genotyped using Sequence Related Amplified Polymorphisms (SRAP) and Simple Sequence Repeat (SSR) markers for genetic linkage mapping. The evaluation of parents and progeny indicated highly significant differences among the crosses and the parents for all the traits studied. The progeny nested within crosses differed only for genetic color and turfgrass quality in fall. Best linear unbiased prediction (BLUP) showed high improvement potential for lateral spread, genetic color, and spring density. These results support the potential of recombination breeding in identifying transgressive segregants for certain traits of interest in buffalograss genotypes. The genotypes (diploids, tetraploids, pentaploid, and hexaploids) and the progeny evaluated for chinch bug resistance had highly significant differences for chinch bug damage ratings. The genotypes were categorized into moderately resistant to moderately susceptible types. Genotypes NE 3297, 196, 184, Bowie, and Legacy were moderately resistant with a damage rating of \u3e1, but \u3c3, while NE 2990, NE 2838, and 1-57-19 were moderately susceptible with a damage rating of≥3, but \u3c4. The susceptible genotypes, NE 2990, NE 2838, and 378, had area under the chinch bug damage progress curve ranging from 88.2 to 78.1, while the resistant genotypes, Prestige, NE 3297 and NE 196, had values of 53.7 to 59.2. There was no relationship between ploidy level of the genotypes and chinch bug resistance. The progeny were segregated into one highly resistant, 78 progeny (83%) moderately resistant, 13 (14%) moderately susceptible, and two highly susceptible types. This response is a strong indication that chinch bug resistance can be improved by hybridization. Morphological traits such as leaf and stolon internodes length were highly variable, indicating a strong potential of slow growth and reduced mowing in buffalograss, but had no impact on chinch bug resistance of the progeny evaluated. The co-segregation analysis of the marker data placed 42 markers into nine discrete linkage groups covering 355.10 cM, with linkage group sizes ranging from 10 cM to 119.78 cM. A range of 2 to 18 loci per linkage group were mapped with an average map distance between two consecutive markers of 12.68 cM. This linkage group would be a rational starting point for further delineation of the buffalograss linkage map with more markers, and could serve as an anchor for genome sequencing. Results from this study lay a foundation for a new direction for buffalograss breeding research that will aid further study and improvement of turfgrass quality and pest resistance