Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes

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Abstract

Cultivated potato ( Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool–mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%–7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5–1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate–late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.

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Second-generation PLINK: rising to the challenge of larger and richer datasets

Christopher Chang, Carson Chow, Laurent Tellier … (2015)

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

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Fast and accurate long-read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2010)

Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.

N Saitou, M Nei (1987)

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

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Author and article information

Contributors

Bourlaye Fofana: URI : https://loop.frontiersin.org/people/438335/overviewRole: Role: Role: Role: Role: Role: Role: Role: Role:

Braulio Soto-Cerda: URI : https://loop.frontiersin.org/people/2536704/overviewRole: Role: Role:

Moshin Zaidi: Role: Role:

David Main: Role: Role:

Sherry Fillmore: Role: Role:

Journal

Journal ID (nlm-ta): Front Genet

Journal ID (iso-abbrev): Front Genet

Journal ID (publisher-id): Front. Genet.

Title: Frontiers in Genetics

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-8021

Publication date (Electronic): 31 January 2024

Publication date Collection: 2023

Volume: 14

Electronic Location Identifier: 1306519

Affiliations

[1] ¹ Charlottetown Research and Development Centre , Agriculture and Agri-Food Canada , Charlottetown, PE, Canada

[2] ² Departamento de Ciencias Agropecuarias y Acuícolas , Universidad Católica de Temuco , Temuco, Chile

[3] ³ Núcleo de Investigación en Producción Alimentaria , Facultad de Recursos Naturales , Universidad Católica de Temuco , Temuco, Chile

[4] ⁴ Kentville Research and Development Centre , Agriculture and Agri-Food Canada , Kentville, NS, Canada

Author notes

Edited by: Leonardo Alfredo Ornella, Cubiqfoods SL, Spain

Reviewed by: Yingpeng Han, Northeast Agricultural University, China

Sajid Shokat, International Atomic Energy Agency, Austria

*Correspondence: Bourlaye Fofana, bourlaye.fofana@ 123456agr.gc.ca

Article

Publisher ID: 1306519

DOI: 10.3389/fgene.2023.1306519

PMC ID: 10864671

PubMed ID: 38357658

SO-VID: b4925176-7a39-4399-a72a-e7b9b0adbd14

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 03 October 2023

Date accepted : 18 December 2023

Funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by Agriculture and Agri-Food Canada under A-base projects J-00076 and J-002665.

Custom metadata

section-at-acceptance Genomics of Plants and the Phytoecosystem

ScienceOpen disciplines: Genetics

Keywords: diploid potato,climate change,drought,maturity,gwas,candidate genes

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ScienceOpen disciplines: Genetics

Keywords: diploid potato, climate change, drought, maturity, gwas, candidate genes

Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes

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Climate Change: Open Access

Most cited references 90

Second-generation PLINK: rising to the challenge of larger and richer datasets

Fast and accurate long-read alignment with Burrows–Wheeler transform

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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