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Öğe Common bean as a potential crop for future food security: An overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics(Taylor & Francis, 2021) Nadeem, Muhammad Azhar; Yeken, Mehmet Zahit; Shahid, Muhammad Qasim; Habyarimana, Ephrem; Yılmaz, Hilal; Alsaleh, Ahmad; Hatipoğlu, Rüştü; Çilesiz, Yeter; Khawar, Khalid Mahmood; Ludidi, Ndiko; Ercişli, Sezai; Aasim, Muhammad; Karaköy, Tolga; Baloch, Faheem ShahzadCommon bean is an important legume crop having high quality protein, micronutrients, vitamins and antioxidants, which makes it a "grain of hope" for poor communities. Hence, a good number of breeding activities have been performed on the improvement of various key traits for years. However, recent advancements in molecular markers, sequencing technologies and the completion of the common bean genome sequence have opened numerous opportunities for fine mapping and gene characterization. The availability of these tools together with investigations of quantitative trait loci (QTL) and candidate genes for key traits such as morpho-agronomic, iron and zinc contents, cooking and quality traits, antioxidant activity, biotic and abiotic stresses pave the way to the development of new strategies for common bean genetic improvement. As a food source, it can contribute to the reduction of food scarcity worldwide in the coming years. Therefore, it is very important to take synergic efforts to integrate common bean genetic and genomic resources in breeding activities to ensure food security and contribute significantly to improved livelihoods in developing countries. Moreover, Kompetitive allele specific PCR (KASP) and CRISPR-Cas9 should be used to develop climate resilience common bean varieties. Here, we provide an overview of the evolution of common bean research by highlighting the past and recent advances in genomics, transgenics, transcriptomics and proteomics and also critically discuss the future prospects for further genetic improvement and better expansion of this crop.Öğe Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line(2019) Ghourı, Fozia; Zhu, Jiani; Yu, Hang; Wu, Jinwen; Baloch, Faheem Shahzad; Liu, Xiangdong; Shahid, Muhammad QasimAutotetraploid rice is a new germplasm resource obtained by doubling chromosomes through colchicine treatment. There have been many studies on the reproductive characteristics of autotetraploid rice, but little is known about global DNA variations and reasons for low embryo sac fertility in autotetraploid rice. Therefore, an autotetraploid rice line (T446) was used for resequencing and embryo sac fertility was observed. Whole-genome resequencing data revealed 87,229 SNPs and 11,022 InDels in the genome of T446 versus E246 (diploid rice), which had an average of 23.37 SNPs and 2.95 InDels per 100 kb. A total of 17,375 and 17,171 structural variations and 131 and 128 copy number variations were identified in the autotetraploid and its diploid counterpart, respectively. We detected 140 large-effects SNPs and InDel variants that might be related to the embryo sac fertility of autotetraploid rice, including 10 genes that may be closely associated with the development of the embryo sac. Of these, Os02g0292600 and Os06g0565200 were specifically expressed in the ovary. Mature embryo sac fertility was observed through whole-mount eosin B-staining confocal laser scanning microscopy. Many abnormalities were found in the embryo sac of T446, including embryo sac degeneration, embryo sac without female germ unit, abnormal polar nuclei, and poly-eggs, which, in turn, resulted in low seed set. However, whole-genome polymorphisms and genetic differences were high and exhibited broad prospects for genetic improvement. Genetic mutations in genes associated with embryo sac fertility in polyploid rice require further studies.Öğe Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome(Springer Heidelberg, 2019) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Ercişli, Sezai; Baloch, Faheem ShehzadTianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.Öğe DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing(Taylor & Francis Ltd, 2018) Nadeem, Muhammad Azhar; Nawaz, Muhammad Amjad; Shahid, Muhammad Qasim; Doğan, Yıldız; Cömertpay, Gönül; Yıldız, Mehtap; Hatipoğlu, RüştüWith the development of molecular marker technology in the 1980s, the fate of plant breeding has changed. Different types of molecular markers have been developed and advancement in sequencing technologies has geared crop improvement. To explore the knowledge about molecular markers, several reviews have been published in the last three decades; however, all these reviews were meant for researchers with advanced knowledge of molecular genetics. This review is intended to be a synopsis of recent developments in molecular markers and their applications in plant breeding and is devoted to early researchers with a little or no knowledge of molecular markers. The progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers and provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies have facilitated the identification of novel genetic markers for complex and unstructured populations. Altogether, the history, the types of markers, their application in plant sciences and breeding, and some recent advancements in genomic selection and genome editing are discussed.Öğe Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci : for conservation of soybean germplasm(Pergamon-Elsevier Science Ltd, 2015) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem Shehzad; Wang, YingGenetic diversity and its geographical patterns play a very important role in species conservation and exploitation. Here, nucleotide polymorphism patterns of four single copy nuclear gene loci in wild (Glycine soja) and cultivated soybean (Glycine max) populations from different geographical regions as well as their demographic history were analyzed. The results showed that: (1) Southern subpopulation has the highest, while central subpopulation revealed the lowest genetic diversity among three Chinese G. soja subpopulations. (2) Northern Chinese G. max subpopulation depicted higher genetic diversity than other two Chinese, Korean, Japanese and American G. max subpopulations. (3) Significant genetic differentiation (P < 0.001) was observed among Chinese G. soja subpopulations from three ecological zones. There was also a significant genetic differentiation ( P < 0.01) between three Chinese and Japanese subpopulations of G. max. (4) The demographic dynamics revealed that effective population size of G. soja is expanding, while it was constant in G. max. G. soja is a useful germplasm resource to widen the genetic diversity of G. max. This study suggests that native populations of G. soja from different geo-ecological regions should be protected to conserve the genetic diversity. (C) 2015 Elsevier Ltd. All rights reserved.Öğe The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences(Pergamon-Elsevier Science Ltd, 2017) Wang, Yunsheng; Ghouri, Fozia; Shahid, Muhammad Qasim; Naeem, Muhammad; Baloch, Faheem ShehzadGlycine sofa, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. sofa exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions. (C) 2017 Elsevier Ltd. All rights reserved.Öğe Genetic diversity in mutated and non-mutated rice varieties(Funpec-Editora, 2015) Naeem, Muhammad; Ghouri, Fozia; Shahid, Muhammad Qasim; Iqbal, Mudassar; Baloch, Faheem ShehzadWe studied the genetic variability due to mutation induced by gamma-rays (10, 15, and 20 Kr) on various traits of twelve rice genotypes. Mutated and non-mutated seeds were sown in the field between July 2013 and 2014 using a split plot design. Yield and yield-related trait data was recorded, which showed significant (P < 0.05) genotypic and irradiation effects. Gamma radiation exerted non-significant effects on the panicle length of all plants, indicating the uniformity of performance of this character at different radiation levels. The plant height, grains per main panicle, panicle length, 1000-grain weight, grain weight per main panicle, and fertility percentage was minimum in Basmati-198, Basmati-Pak, Shaheen-2000, Super Basmati, Basmati-385, and Super Basmati, respectively, when exposed to radiation at 20 Kr. However, Basmati-370 attained maximum flag leaf area at this level of radiation. Broad sense heritability ranged from 72.0 to 97.7%, indicating the possibility of selection during earlier generations. Phenotypic correlation was positive and significant between grain weight per main panicle with panicle length and flag leaf area. Number of grains per main panicle and genotypic correlation were positive among grain weight per main panicle, panicle length, fertility percentage, 1000-grain weight, and plant height, indicating the effectiveness of these traits in the selection for yield. Phylogenetic analyses revealed a pair-wise similarity ranging from 0.51-0.76 before mutation and 0.39-0.89 after mutation. This study proved that gamma-rays at 20 Kr would be most effective in creating genetic variability in the existing germplasm.Öğe Identification, phylogenetic analysis, and expression patterns of the SAUR gene family in loquat (Eriobotrya Japonica)(2020) Gan, Xiaoqing; Jing, Yi; Shahid, Muhammad Qasim; He, Yehua; Baloch, Faheem ShahzadSmall auxin-up RNAs (SAURs) are the most frequent and primary auxin responsive genes, and they are commonly used as early auxin-responsive markers. Until now, no SAUR gene has been identified in Eriobotrya plants. In this study, we used Arabidopsis SAUR sequences as a query to search against the loquat genome sequence. In total, we obtained 57 SAUR genes in loquat, hereafter referred to as Eriobotrya japonica SAUR (EjSAUR) genes, which ranged from 267 to 735 bp in the coding sequence with predicted proteins of 88–244 aa. A total of 47 EjSAUR genes were distributed on 11 chromosomes of the loquat genome. Based on their physical positions, 80.9% (38 of 47) of the EjSAUR genes were clustered together on the loquat chromosomes, suggesting that tandem duplicate genes might be the major mechanism for the expansion of this family. The expression analysis displayed high expression divergence among the different organs, which suggested that EjSAUR genes may play an important role in different organs. These results laid a foundation for the functional validation of EjSAUR genes in Eriobotrya plants.Öğe Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset(Bmc, 2020) Wang, Yunsheng; Nie, Fei; Shahid, Muhammad Qasim; Baloch, Faheem ShehzadBackgroundBoth selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species.ResultsWe identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species.ConclusionSome important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.Öğe De novo assembly and annotation of the juvenile tuber transcriptome of agastrodia elatahybrid by rna sequencing: Detection of ssr markers(Springer/Plenum Publishers, 2020) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem ShehzadGastrodia elatais a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of aG. elatahybrid (Gastrodia elata BI.f.elata x Gastrodia elata BI.f.pilifera) by using Illumina HiSeq (TM) 4000 sequencing platform. De novo assembly and bioinformatics analysis revealed 20,237,474 clean reads, including 2,529,684,250 bp that assembled into 34,323 unigenes with an average length of 695.19 bp. Among them, 24,698 (71.96%) unigenes were annotated by at least one of the Nr, Swiss-Prot, COG and KEGG databases. A total of 4236 (12.34%) unigenes were identified as candidate transcription factors, and 2007 (5.85%) unigenes were found to contain at least one single sequence repeat (SSR). Of these SSRs, AG/CT repeat motif was the most frequent, with a total of 498 (21.67%). This study will enhance our understanding about the molecular mechanism of physiological metabolism, growth and development ofG. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.Öğe Phylogeographical studies of Glycine soja: implicating the refugium during the Quaternary glacial period and large-scale expansion after the Last Glacial Maximum(Tubitak Scientific & Technological Research Council Turkey, 2016) Wang, Yunsheng; Shahid, Muhammad Qasim; Baloch, Faheem ShehzadWild soybean (Glycine soja Sieb. & Zucc.), the progenitor of cultivated soybean (Glycine max (L.) Merr.), is widely distributed in the Sino-Japanese Floristic Region (SJFR). Therefore, it is an excellent model organism to study the effect of Quaternary climatic changes on the distribution and migration of plant taxa in the SJFR. To investigate the phylogeography of G. soja, a total of 632 individuals representing 52 populations throughout the species distribution range were genotyped by using the sequencing data of a nuclear locus, AF105221, and a chloroplast locus, trnQ-rps16. We detected a total of 23 haplotypes from two loci, including five common and 18 rare haplotypes. Among them, 17 rare haplotypes were limited to Northeast Asia (Northeast China (NEC) and Korea) and the Yangzi River basin (middle and downstream of the Yangzi River (MDYR) and the eastern end of Southwest China (SWC)). Moreover, two common haplotypes were detected throughout the species distribution wide range. All the haplotypes from Japan and the Korean peninsula were also found in China. The haplotype distribution patterns of the two loci suggested that Northeast Asia (NEC and Korea) and the Yangzi River basin (MDYR and the eastern end of SWC) might have been the refugia for G. soja during the Quaternary glacial period, and G. soja expanded rapidly after the end of the Last Glacial Maximum. There was a land bridge between East China, the Korean peninsula, and Japan that permitted gene flow among populations of these regions in the ice age during the Quaternary.Öğe RNA-seq reveals differential expression patterns of genes associated with carotenoid accumulation in loquat(Springer Heidelberg, 2017) Zheng, Ting-ting; Zhang, Zhi-ke; Shahid, Muhammad Qasim; Wei, Wei-ling; Baloch, Faheem ShehzadLoquat (Eriobotrya japonica Lindl.) cultivars can be classified as yellow- and white-fleshed based on fruit color. The pulps of yellow-fleshed cultivars appear yellow because of high contents of carotenoids, while the pulps of white-fleshed cultivars appear ivory white due to the lack of carotenoid accumulation. To elucidate the genes associated with the carotenoid accumulation, de novo assembly of the fruit transcriptome in three loquat cultivars having different pulp colors, including 'Golden nugget' (yellow pulp), 'Jiefangzhong' (yellow pulp), and 'Baiyu' (white pulp), at breaker stage, was conducted in this study. By RNA-seq, a total of 11.92 Gb clean data was obtained, and 51,934 unigenes were assembled and annotated. Based on BLAST search, 26,447 unigenes had a hit in at least one of the protein and nucleotide databases used in the present study. Swiss-Port annotation and Clusters of Orthologous Group were assigned for 16,679 and 13,986 unigenes, respectively. Moreover, Gene Ontology enrichment analysis classified 18,842 unigenes into 53 functional groups, which largely detected in biological process category, followed by cellular component category and molecular function category. We detected 3438 differentially expressed genes using Reads Per kb per Million reads method. Of these genes, six were identified as carotenoid accumulation-related genes. Our study revealed a certain relationship between carotenoid accumulation and expression patterns of carotenogenic genes.Öğe Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops(Public Library Science, 2019) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Ercişli, Sezai; Baloch, Faheem Shehzad; Nie, FeiBlueberry is a kind of new rising popular perennial fruit with high healthful quality. It is of utmost importance to develop new blueberry varieties for different climatic zones to satisfy the demand of people in the world. Molecular marker assisted breeding is believed to be an ideal method for the development of new blueberry varieties for its shorter breeding cycle than the conventional breeding. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers are widely used molecular tools for marker assisted breeding, which could be detected at large scale by the transcriptome sequencing. Here, we sequenced the leaves transcriptome of 19 rabbiteye (Vaccinium ashei Reade), 13 southern highbush (Vaccinium. corymbosum L x native southern Vaccinium Spp) and 22 cultivars of northern highbush blueberry (Vaccinium corymbosum L) by using next generation sequencing technologies. A total of 80.825 Gb clean data with an average of about 12.525 million reads per cultivar were obtained. We assembled 58,968, 55,973 and 53,887 unigenes by using the clean data from rabbiteye, southern highbush and northern highbush blueberry cultivars, respectively. Among these unigenes, 3599, 3495 and 3513 unigenes were detected as candidate resistance genes in three blueberry crops. Moreover, we identified more than 8756, 9020, and 9198 SSR markers from these unigenes, and 7665, 4861, 13,063 SNPs from the annotated single copy unigenes, respectively. The results will be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry, and would also offer huge number of molecular tools for the marker assisted breeding to produce blueberry cultivars with different adaptive characteristics.Öğe A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from Central Fertile Crescent(Public Library Science, 2017) Baloch, Faheem Shehzad; Alsaleh, Ahmad; Shahid, Muhammad Qasim; Çiftçi, Vahdettin; de Miera, Luis E. Saenz; Nadeem, Muhammad AzharUntil now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers' small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis. A total of 39,568 DArTseq and 20,661 SNP markers were used to characterize the genetic characteristic of 91 durum wheat land races. Clustering based on Neighbor joining analysis, principal coordinate as well as Bayesian model implemented in structure, clearly showed that the grouping pattern is not associated with the geographical distribution of the durum wheat due to the mixing of the Turkish and Syrian landraces. Significant correlation between DArTseq and SNP markers was observed in the Mantel test. However, we detected a non-significant relationship between geographical coordinates and DArTseq (r = -0.085) and SNP (r = -0.039) loci. These results showed that unconscious farmer selection and lack of the commercial varieties might have resulted in the exchange of genetic material and this was apparent in the genetic structure of durum wheat in Turkey and Syria. The genomic characterization presented here is an essential step towards a future exploitation of the available durum wheat genetic resources in genomic and breeding programs. The results of this study have also depicted a clear insight about the genetic diversity of wheat accessions from the Central Fertile Crescent.
