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Genomewide SNP Identification and Use for Resolving Population Structure and...
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Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest Volume II

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 10517

Special Issue Editors

Prof. Dr. Umesh K. Reddy

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Guest Editor
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
Interests: GWAS; QTL mapping of key traits; population genetics; functional genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Suhas Shinde

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Guest Editor
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
Interests: plant stress biology; plant environment interaction; functional genomics; natural variation; and GWAS
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Padma Nimmakayala

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Guest Editor
Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
Interests: genomics; genetic diversity; abiotic stress; phytoremediation; breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Purushothaman Natarajan

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Guest Editor
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
Interests: genomics; bioinformatics; plant science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the merging of methodologies for making reduced-representation/resequencing libraries, RNAseq, next-generation sequencing and bioinformatic approaches have recently emerged for identifying genome-wide SNPs and insertions/deletions (InDELs) for resolving population structure, along with genome-wide association studies (GWAS), QTL/eQTL mapping, and bulk segregant analysis, which can be used to identify genomic regions of interest. These reduced-representation and resequencing methods are currently having great impacts in studying novel and existing genetic variation for various crop-improvement programs as well as model and non-model plants of ecological significance. In Volume II, we expand the scope of functional genomics involving RNAseq and qRT-PCR validations targeting mapped traits of interest. 

The purpose of this Special Issue is to publish high-quality research papers as well as review articles addressing recent studies involving SNP mining, resolving population structures, haplotype networking, and GWAS as emerging tools for plant breeding and ecology research. Original, high-quality contributions that have not yet been published or that are not currently under review by other journals or peer-reviewed conferences are sought.

Prof. Dr. Umesh K. Reddy
Dr. Suhas Shinde
Prof. Dr. Padma Nimmakayala
Dr. Purushothaman Natarajan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SNP mining and InDELs
  • Population structure analysis
  • GWAS
  • High-density QTL mapping
  • Haplotype networking
  • Genomics of wild crop relatives

Published Papers (3 papers)

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Research

20 pages, 5004 KiB  
Article
RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars
by Saranya Chandrasekar, Purushothaman Natarajan, Priyank Hanuman Mhatre, Mahesh Mahajan, Sundararaj Nivitha, Venkatasalam E. Palanisamy, Umesh K. Reddy and Palanisamy Sundararaj
Plants 2022, 11(8), 1008; https://doi.org/10.3390/plants11081008 - 07 Apr 2022
Cited by 5 | Viewed by 2510
Abstract
Potato (Solanum tuberosum L.) is an important food crop worldwide, and potato cyst nematodes (PCNs) are among the most serious pests. The identification of disease resistance genes and molecular markers for PCN infestation can aid in crop improvement research programs against PCN [...] Read more.
Potato (Solanum tuberosum L.) is an important food crop worldwide, and potato cyst nematodes (PCNs) are among the most serious pests. The identification of disease resistance genes and molecular markers for PCN infestation can aid in crop improvement research programs against PCN infestation. In the present study, we used high-throughput RNA sequencing to investigate the comprehensive resistance mechanisms induced by PCN infestation in the resistant cultivar Kufri Swarna and the susceptible cultivar Kufri Jyoti. PCN infestation induced 791 differentially expressed genes in resistant cultivar Kufri Swarna, comprising 438 upregulated and 353 downregulated genes. In susceptible cultivar Kufri Jyoti, 2225 differentially expressed genes were induced, comprising 1247 upregulated and 978 downregulated genes. We identified several disease resistance genes (KIN) and transcription factors (WRKY, HMG, and MYB) that were upregulated in resistant Kufri Swarna. The differentially expressed genes from several enriched KEGG pathways, including MAPK signaling, contributed to the disease resistance in Kufri Swarna. Functional network analysis showed that several cell wall biogenesis genes were induced in Kufri Swarna in response to infestation. This is the first study to identify underlying resistance mechanisms against PCN and host interaction in Indian potato varieties. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest Volume II)
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13 pages, 3081 KiB  
Article
Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.)
by Ramesh Palakurthi, Veera Jayalakshmi, Yogesh Kumar, Pawan Kulwal, Mohammad Yasin, Nandkumar Surendra Kute, Chinchole Laxuman, Sharanabasappa Yeri, Anilkumar Vemula, Abhishek Rathore, Srinivasan Samineni, Khela Ram Soren, Biswajit Mondal, Girish Prasad Dixit, Chellapilla Bharadwaj, Sushil K. Chaturvedi, Pooran M. Gaur, Manish Roorkiwal, Mahendar Thudi, Narendra P. Singh and Rajeev K. Varshneyadd Show full author list remove Hide full author list
Plants 2021, 10(12), 2583; https://doi.org/10.3390/plants10122583 - 25 Nov 2021
Cited by 2 | Viewed by 2286
Abstract
The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. [...] Read more.
The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest Volume II)
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22 pages, 14439 KiB  
Article
Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits
by Bartholomew Saanu Adeleke, Ayansina Segun Ayangbenro and Olubukola Oluranti Babalola
Plants 2021, 10(9), 1776; https://doi.org/10.3390/plants10091776 - 26 Aug 2021
Cited by 28 | Viewed by 4806
Abstract
Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower [...] Read more.
Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower in South Africa has not been studied. Therefore, we present whole-genome sequence of agriculturally important B. cereus strain T4S isolated from sunflower plants. The NextSeq Illumina sequencing yielded 7,255,762 bp sequence reads, 151 bp average read length, 5,945,881 bp genome size, 56 tRNA, 63 rRNA, and G + C content of 34.8%. The phylogeny analysis of strain T4S was similar to B. cereus NJ-W. Secondary metabolites, such as petrobactin, bacillibactin, bacitracin, molybdenum factor, zwittermicin, and fengycin underlining bacterial biocontrol efficacy against phytopathogens were found in the T4S genome. The predicted novel genes in the bacterial genome mediating the complex metabolic pathways can provide a genetic basis in understanding endosphere biology and their multiple functions thereof in crop improvement. Interestingly, seed and root inoculation with strain T4S contributed to sunflower yield under greenhouse experiments. Hence, the detection of notable genes specific for plant growth promotion as validated under in vitro screening, promisingly, suggests the relevance of strain T4S in agricultural biotechnology. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest Volume II)
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