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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

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 13479

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 merger of methodologies for making reduced representation libraries, Nextgen sequencing and bioinformatic approaches have emerged recently to identify genomewide SNPs and Insertion/Deletion (InDELs) for resolving population structure and genome-wide association studies (GWAS), QTL mapping, and bulk segregant analysis that can be used to identify genomic regions of interest. These reduced representation methods currently have great impact in studying novel and existing genetic variation for various crop improvement programs as well as non-model plants that have ecological significance.

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 structure, haplotype networking, and GWAS as emerging tools for plant breeding and ecology research. Original, high-quality contributions that are not yet 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 crop wild relatives

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Published Papers (3 papers)

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17 pages, 3427 KiB  
Article
Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics
by Bandana Ghimire, Thangasamy Saminathan, Abiodun Bodunrin, Venkata Lakshmi Abburi, Arjun Ojha Kshetry, Suhas Shinde, Padma Nimmakayala and Umesh K. Reddy
Plants 2021, 10(2), 191; https://doi.org/10.3390/plants10020191 - 20 Jan 2021
Cited by 2 | Viewed by 3297
Abstract
Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We [...] Read more.
Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest)
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17 pages, 1681 KiB  
Article
Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions
by Camilo E. Valenzuela, Paulina Ballesta, Sunny Ahmar, Sajid Fiaz, Parviz Heidari, Carlos Maldonado and Freddy Mora-Poblete
Plants 2021, 10(1), 148; https://doi.org/10.3390/plants10010148 - 13 Jan 2021
Cited by 18 | Viewed by 4139
Abstract
The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide [...] Read more.
The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of Eucalyptus cladocalyx, a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as GEM-related 5 and prohibitin-3, were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest)
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12 pages, 1984 KiB  
Article
Genome-Wide Association Analysis Identifies Candidate Genes Regulating Seed Number per Silique in Arabidopsis thaliana
by Huan-Li Jiang, Jun Hong, Yu-Tong Jiang, Shi-Xia Yu, Yan-Jie Zhang, Jian-Xin Shi and Wen-Hui Lin
Plants 2020, 9(5), 585; https://doi.org/10.3390/plants9050585 - 2 May 2020
Cited by 12 | Viewed by 5121
Abstract
Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, [...] Read more.
Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, genome-wide association analysis (GWAS) was employed to identify the candidate genes regulating SNS. GWAS-based genotype and phenotype association analysis identified 38 most significant SNPs marker sites that were mapped to specific chromosomal positions and allowed us to screen for dozens of candidate genes. One of them (PIN3) was selected for functional validation based on gene expression analysis. It is a positive regulator of Arabidopsis SNS. Although silique length of PIN3 loss of function mutant was not significantly changed, its SNS and seed density (SD) were significantly reduced as compared with the wild type. Notably, PIN3 overexpression lines driven by a placenta-specific promoter STK exhibited significantly shorter siliques, slightly reduced SNS, but significant increased SD compared with wild type, suggesting that PIN3 positively regulates SD through inducing ovule primordia initiation regardless of the placenta size. Ovule initiation determines the maximal possibility of SNS, and new genes and mechanism regulating SNS through modulating ovule initiation is worth further investigated. Full article
(This article belongs to the Special Issue Genomewide SNP Identification and Use for Resolving Population Structure and GWAS of Traits of Interest)
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