Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

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Abstract

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.

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Most cited references 29

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NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis.

Nobutaka Mitsuda, Akira Iwase, Hiroyuki Yamamoto … (2007)

Wood is formed by the successive addition of secondary xylem, which consists of cells with a conspicuously thickened secondary wall composed mainly of lignin and cellulose. Several genes involved in lignin and cellulose biosynthesis have been characterized, but the factors that regulate the formation of secondary walls in woody tissues remain to be identified. In this study, we show that plant-specific transcription factors, designated NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis thaliana. In nst1-1 nst3-1 double knockout plants, the secondary wall thickenings in interfascicular fibers and secondary xylem, except for vascular vessels, were completely suppressed without affecting formation of cells destined to be woody tissues. Conversely, as shown previously for NST1, overexpression of NST3 induced ectopic secondary wall thickenings in various aboveground tissues. Furthermore, the expression of chimeric repressors derived from NST1 and NST3 suppressed secondary wall thickenings in the presumptive interfascicular fibers. Because putative orthologs of NST1 and NST3 are present in the genome of poplar, our results suggest that they are also key regulators of the formation of secondary walls in woody plants and could be used as a tool for the genetic engineering of wood and its derivatives.

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SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis.

S Liljegren, G Ditta, Y Eshed … (2000)

The fruit, which mediates the maturation and dispersal of seeds, is a complex structure unique to flowering plants. Seed dispersal in plants such as Arabidopsis occurs by a process called fruit dehiscence, or pod shatter. Few studies have focused on identifying genes that regulate this process, in spite of the agronomic value of controlling seed dispersal in crop plants such as canola. Here we show that the closely related SHATTERPROOF (SHP1) and SHATTERPROOF2 (SHP2) MADS-box genes are required for fruit dehiscence in Arabidopsis. Moreover, SHP1 and SHP2 are functionally redundant, as neither single mutant displays a novel phenotype. Our studies of shp1 shp2 fruit, and of plants constitutively expressing SHP1 and SHP2, show that these two genes control dehiscence zone differentiation and promote the lignification of adjacent cells. Our results indicate that further analysis of the molecular events underlying fruit dehiscence may allow genetic manipulation of pod shatter in crop plants.

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Accurate prediction of genetic values for complex traits by whole-genome resequencing.

Theo Meuwissen, Mike Goddard (2010)

Whole-genome resequencing technology has improved rapidly during recent years and is expected to improve further such that the sequencing of an entire human genome sequence for $1000 is within reach. Our main aim here is to use whole-genome sequence data for the prediction of genetic values of individuals for complex traits and to explore the accuracy of such predictions. This is relevant for the fields of plant and animal breeding and, in human genetics, for the prediction of an individual's risk for complex diseases. Here, population history and genomic architectures were simulated under the Wright-Fisher population and infinite-sites mutation model, and prediction of genetic value was by the genomic selection approach, where a Bayesian nonlinear model was used to predict the effects of individual SNPs. The Bayesian model assumed a priori that only few SNPs are causative, i.e., have an effect different from zero. When using whole-genome sequence data, accuracies of prediction of genetic value were >40% increased relative to the use of dense approximately 30K SNP chips. At equal high density, the inclusion of the causative mutations yielded an extra increase of accuracy of 2.5-3.7%. Predictions of genetic value remained accurate even when the training and evaluation data were 10 generations apart. Best linear unbiased prediction (BLUP) of SNP effects does not take full advantage of the genome sequence data, and nonlinear predictions, such as the Bayesian method used here, are needed to achieve maximum accuracy. On the basis of theoretical work, the results could be extended to more realistic genome and population sizes.

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Author and article information

Contributors

Manoj Prasad: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2014

Publication date (Electronic): 9 July 2014

Volume: 9

Issue: 7

Electronic Location Identifier: e101673

Affiliations

[1 ]Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia

[2 ]Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia

[3 ]University of Wollongong, Wollongong, NSW, Australia

[4 ]NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia

[5 ]Australian Centre for Plant Functional Genomic, School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia

[6 ]School of Plant Biology, University of Western Australia, Perth, WA, Australia

[7 ]CSIRO Division of Plant Industries, Canberra, ACT, Australia

[8 ]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India

[9 ]Agriculture and Agri-Food Canada, Saskatoon, Canada

[10 ]School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia

National Institute of Plant Genome Research, India

Author notes

* E-mail: harsh.raman@ 123456dpi.nsw.gov.au

Competing Interests: DArT P/L (Canberra, Australia) is a genotyping company and may benefit from providing genotyping service to the Brassica R&D community. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

Conceived and designed the experiments: HR RR. Analyzed the data: HR RR SD NC AK FD. Wrote the paper: HR RR. Reviewed and approved the manuscript: HR RR AK FD JC NC SD GK DE MM PR IAPP JB DL NW. Supervised the project: HR RR. Performed genotyping with SSR, DArT, SNP and DArT-SeqTM markers: RR HR AK. Phenotyped the populations for shatter resistance using pendulum test: RR GK HR. Conducted field experiments: RR HR DL. Provided C genome scaffold data: IAPP. Performed in silico mapping of sequenced markers with A and C genome scaffolds: HR AK FD JC. Performed in silico mapping of known pod shattering genes using reference A and C genomic sequences: DE PR JB. Aligned and integrated all genomic and physical map information for comparative mapping and LD: HR RR. Performed anatomical analysis: MM RR GB HR. Conducted alien gene introgression work: GK. Constructed a DH population from BLN2762/Surpass400: NW. Identified a set of diversity panel for GWAS: HR NW.

Article

Publisher ID: PONE-D-13-48808

DOI: 10.1371/journal.pone.0101673

PMC ID: 4090071

PubMed ID: 25006804

SO-VID: 962cf777-d4a7-434b-a4db-7c307bb1a00f

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 20 November 2013

Date accepted : 2 June 2014

Page count

Pages: 13

Funding

This work was funded by the Australian Grains Research and Development Corporation (research project DAN00117). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

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Most cited references 29

NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis.

SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis.

Accurate prediction of genetic values for complex traits by whole-genome resequencing.

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