Comparison of biometrical models for joint linkage association mapping

Abstract Key message A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Abstract Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differentiate winter, semi-winter and spring ecotypes. However, because these are generally fixed in locally adapted genotypes, they have only limited relevance for fine adjustment of flowering time in elite cultivar gene pools. In crosses between ecotypes, the ecotype-specific major-effect mutations mask minor-effect loci of interest for breeding. Here, we investigated flowering time in a multiparental mapping population derived from seven elite winter oilseed rape cultivars which are fixed for major-effect mutations separating winter-type rapeseed from other ecotypes. Association mapping revealed eight genomic regions on chromosomes A02, C02 and C03 associating with fine modulation of flowering time. Long-read genomic resequencing of the seven parental lines identified seven structural variants coinciding with candidate genes for flowering time within chromosome regions associated with flowering time. Segregation patterns for these variants in the elite multiparental population and a diversity set of winter types using locus-specific assays revealed significant associations with flowering time for three deletions on chromosome A02. One of these was a previously undescribed 288 bp deletion within the second intron of FLOWERING LOCUS T on chromosome A02, emphasizing the advantage of long-read sequencing for detection of structural variants in this size range. Detailed analysis revealed the impact of this specific deletion on flowering-time modulation under extreme environments and varying day lengths in elite, winter-type oilseed rape.

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Genome-wide association mapping in maize: status and prospects

3 Biotech ◽

10.1007/s13205-021-02799-4 ◽

2021 ◽

Vol 11 (5) ◽

Author(s):

Kumari Shikha ◽

J. P. Shahi ◽

M. T. Vinayan ◽

P. H. Zaidi ◽

A. K. Singh ◽

...

Keyword(s):

Association Mapping ◽

Genome Wide Association ◽

Genome Wide

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Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping

Plants ◽

10.3390/plants10010010 ◽

2020 ◽

Vol 10 (1) ◽

pp. 10

Author(s):

Sebastian Zahn ◽

Thomas Schmutzer ◽

Klaus Pillen ◽

Andreas Maurer

Keyword(s):

Quantitative Trait Loci ◽

Association Mapping ◽

Cross Section ◽

Quantitative Trait ◽

Spring Barley ◽

Raw Material ◽

Total Thickness ◽

Nested Association Mapping ◽

Elite Cultivar ◽

Major Qtl

Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP genotyping yielded new insights and a better understanding of the quantitative trait loci (QTL) involved in controlling the peduncle diameter traits, we found the total thickness of peduncle tissues and the area of the peduncle cross-section. We identified three major QTL regions on chromosomes 2H and 3H mainly impacting the traits. Remarkably, the exotic allele at the QTL on chromosome 3H improved all three traits investigated in this work. Introgressing this QTL in elite cultivars might facilitate to adjust peduncle morphology for improved plant stability or enlarged straw biomass production independent of flowering time and without detrimental effects on grain yield.

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Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-082 ◽

2010 ◽

Vol 53 (11) ◽

pp. 884-898 ◽

Cited By ~ 31

Author(s):

Jianjun Zhao ◽

Anna Artemyeva ◽

Dunia Pino Del Carpio ◽

Ram Kumar Basnet ◽

Ningwen Zhang ◽

...

Keyword(s):

Association Mapping ◽

Flowering Time ◽

Brassica Rapa ◽

Core Collection ◽

Field Experiments ◽

Research Centre ◽

Candidate Gene Approach ◽

Core Collections ◽

Genome Wide ◽

Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

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