Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate

Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron polymorphism (PIP) markers specific to 3,445 (13.40%) gene models that span 8 Tunisia chromosomes. The ePCR validation of all these PIP markers on the Tunisia genome revealed single-locus amplification for 1,233 (14%) markers corresponding to 958 (27.80%) genes. The markers yielding single amplicons were then mapped onto Tunisia chromosomes to develop a saturated linkage map. The functional categorization of 958 genes revealed them to be a part of the nucleus and the cytoplasm having protein binding and catalytic activity, and these genes are mainly involved in the metabolic process, including photosynthesis. Further, through ePCR, 1,233 PIP markers were assayed on multiple genomes, which resulted in the identification of 886 polymorphic markers with an average PIC value of 0.62. In silico comparative mapping based on physically mapped PIP markers indicates a higher synteny of Tunisia with the Dabenzi and Taishanhong genomes (>98%) in comparison with the AG2017 genome (95%). We then performed experimental validation of a subset of 100 PIP primers on eight pomegranate genotypes and identified 76 polymorphic markers, with 15 having PIC values ≥0.50. We demonstrated the potential utility of the developed markers by analyzing the genetic diversity of 31 pomegranate genotypes using 24 PIP markers. This study reports for the first time large-scale development of gene-based and chromosome-specific PIP markers, which would serve as a rich marker resource for genetic variation studies, functional gene discovery, and genomics-assisted breeding of pomegranate

Improved control strategy of DFIG-based wind turbines using direct torque and direct power control techniques

This paper presents different control strategies for a variable-speed wind energy conversion system (WECS), based on a doubly fed induction generator. Direct Torque Control (DTC) with Space-Vector Modulation is used on the rotor side converter. This control method is known to reduce the fluctuations of the torque and flux at low speeds in contrast to the classical DTC, where the frequency of switching is uncontrollable. The reference for torque is obtained from the maximum power point tracking technique of the wind turbine. For the grid-side converter, a fuzzy direct power control is proposed for the control of the instantaneous active and reactive power. Simulation results of the WECS are presented to compare the performance of the proposed and classical control approaches.Peer reviewedFinal Accepted Versio

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate

Genome-wide characterization and development of simple sequence repeat markers for genetic studies in pomegranate (Punica granatum L.)

The availability of the draft genome sequence of pomegranate cv. Dabenzi presents unprecedented opportunities for the development of largescale genomic resources, such as DNA markers for genotyping applications. In this study, we identify a new set of highly polymorphic simple sequence repeat (SSR) markers by targeting the SSR motif lengths of ≥ 24 bp. A total of 1,73,633 SSRs were identified in the 296-Mb pomegranate genome assembly, reflecting an average density of 527.97 SSRs/Mb. Of these, 43,853 SSRs belong to Class I category (> 20 bp). Concerning the abundance of repeat types in the current dataset, dinucleotide (NN) repeats (31.19%) were the dominant class among all SSRs identified in the genome, followed by tetranucleotide (NNNN: 20.5%) and trinucleotide repeats (NNN: 16.8%). The top two SSR motifs in NN category were AT/AT (64.90%) and AG/CT (28.51%), whereas AAT/ATT (34.66%) and AAG/CTT (28.91%) were the most abundant among NNN repeats. Primer pairs were designed for a total of 2856 Class I SSRs and 110 primers were then assayed initially on eight pomegranate genotypes for polymorphism survey. Polymorphic fragments were obtained for 82 SSRs (77.36%), of which a subset of 13 informative SSRs was further employed to investigate genetic diversity among 46 pomegranate genotypes. Approaches, such as population structure, cluster and PCA elucidated genetic relationships among 46 diverse pomegranate genotypes. In summary, here we developed the first set of genome-wide SSRs in pomegranate that will serve as a powerful genomic tool for future genetic studies. These SSRs have widespread applications in QTL mapping and marker-assisted selection for breeding