Associative transcriptomics of traits in the polyploid crop species Brassica napus

Harper, Andrea L.; Trick, Martin; Higgins, Janet; Fråser, F C; Clissold, Leah; Wells, Rachel; Hattori, Chie; Werner, P.; Bancroft, Ian

doi:10.1038/nbt.2302

Cited by 289 publications

(347 citation statements)

References 33 publications

Supporting

Mentioning

327

Contrasting

Unclassified

Order By: Relevance

“…ePAV-GWAS), corrected for population structure and relatedness, and this should provide additional insights into the architecture and regulation of quantitative traits and help understand certain important biological questions such as adaptation (Hirsch et al 2014;Harper et al 2012). Interestingly, about 15% of the identified ePAVs were found to associate with agronomic and metabolic traits, which confirms the expectation that gene expression presence and absence can affect the phenotypic variation directly.…”

Section: Discussionsupporting

confidence: 64%

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Jin

Liu

et al. 2015

Preprint

View full text Add to dashboard Cite

Variation in gene expression contributes to the diversity of phenotype. The construction of the pan-transcriptome is especially necessary for species with complex genomes, such as maize. However, knowledge of the regulation mechanisms and functional consequences of the pan-transcriptome is limited. In this study, we identified 13,382 nuclear expression presence and absence variation candidates (ePAVs, expressed in 5%~95% lines; based on the reference genome) by re-analyzing the RNA sequencing data from the kernels (15 days after pollination) of 368 maize diverse inbreds. It was estimated that only ~1% of the ePAVs are explained by DNA sequence presence and absence variations (PAV). The ePAV genes tend to be regulated by distant eQTLs when compared with non-ePAV genes (called here core expression genes, expressed in more than 95% lines). When the expression presence/absence status was used as the "genotype" to perform genome-wide association study, 56 (0.42%) ePAVs were significantly associated with 15 agronomic traits and 1,967 (14.74%) with 526 metabolic traits, measured from the mature kernels. While the above was majorly based on the reference genome, by using a modified 'assemble-then-align' strategy, 2,355 high confidence novel sequences with a total length of 1.9Mb were found absent in the current B73 reference genome (v2). Ten randomly selected novel sequences were validated with genomic PCR. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes. Two novel validated sequences annotated as NBS_LRR like genes were found to associate with flavonoid content and their homologs in rice were also found to affect flavonoids and disease-resistance. Novel sequences absent in the present reference genome might be functionally important and deserve more attentions. This study provides novel perspectives and resources to discover maize quantitative trait variations and help us to better understand the kernel regulation networks, thus enhancing maize breeding.

show abstract

Section: Discussionsupporting

confidence: 64%

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Jin

Liu

et al. 2015

Preprint

View full text Add to dashboard Cite

show abstract

“…Understanding the control of nutrient homeostasis is particularly important for crop plants, as it may contribute to improving NUE and the reduction of fertilizer use. Both QTL and GWAS have been used not only in model species but also directly in crops, such as oilseed rape (Ding et al, 2010;Harper et al, 2012). Due to its polyploidy, Brassica napus presents a significant challenge for GWAS, which, however, has been successfully circumvented by using messenger RNA sequencing for the identification of the polymorphic molecular markers in an approach termed associative transcriptomics (AT; Harper et al, 2012).…”

mentioning

confidence: 99%

“…These traits can be analyzed through quantitative trait locus (QTL) analysis (Loudet et al, 2003(Loudet et al, , 2007Harada et al, 2004;Reymond et al, 2006;Habash et al, 2007;Ding et al, 2010) or genome-wide association studies (GWAS; Atwell et al, 2010;Chan et al, 2011;Harper et al, 2012). The usefulness of GWAS has been demonstrated by capturing numerous well-characterized candidate genes (Aranzana et al, 2005;Atwell et al, 2010).…”

mentioning

confidence: 99%

“…Both QTL and GWAS have been used not only in model species but also directly in crops, such as oilseed rape (Ding et al, 2010;Harper et al, 2012). Due to its polyploidy, Brassica napus presents a significant challenge for GWAS, which, however, has been successfully circumvented by using messenger RNA sequencing for the identification of the polymorphic molecular markers in an approach termed associative transcriptomics (AT; Harper et al, 2012). The validity of the approach was demonstrated by the identification of a polymorphism in a MYB28 gene, encoding a transcription factor controlling the synthesis of aliphatic glucosinolates, being responsible for accumulation of the corresponding glucosinolates in seeds (Harper et al, 2012).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Dissection of the Control of Anion Homeostasis by Associative Transcriptomics in Brassica napus

et al. 2014

Self Cite

View full text Add to dashboard Cite

To assess the variation in nutrient homeostasis in oilseed rape and to identify the genes responsible for this variation, we determined foliar anion levels in a diversity panel of Brassica napus accessions, 84 of which had been genotyped previously using messenger RNA sequencing. We applied associative transcriptomics to identify sequence polymorphisms linked to variation in nitrate, phosphate, or sulfate in these accessions. The analysis identified several hundred significant associations for each anion. Using functional annotation of Arabidopsis (Arabidopsis thaliana) homologs and available microarray data, we identified 60 candidate genes for controlling variation in the anion contents. To verify that these genes function in the control of nutrient homeostasis, we obtained Arabidopsis transfer DNA insertion lines for these candidates and tested them for the accumulation of nitrate, phosphate, and sulfate. Fourteen lines differed significantly in levels of the corresponding anions. Several of these genes have been shown previously to affect the accumulation of the corresponding anions in Arabidopsis mutants. These results thus confirm the power of associative transcriptomics in dissection of the genetic control of complex traits and present a set of candidate genes for use in the improvement of efficiency of B. napus mineral nutrition.

show abstract

“…These come from diverse plant families, but share the fact that they have undergone recent hybridisation and whole genome duplication (that is, they are allopolyploids). How the possession of two complete sub-genomes from different parental species might contribute to their high yields is not fully understood, but it certainly does contribute to complexity in bioinformatic analyses of the genomes and transcriptomes of these crops (for example, Harper et al, 2012).…”

mentioning

confidence: 99%

Unravelling gene expression of complex crop genomes

Buggs¹

2012

Heredity

View full text Add to dashboard Cite

Associative transcriptomics of traits in the polyploid crop species Brassica napus

Cited by 289 publications

References 33 publications

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Dissection of the Control of Anion Homeostasis by Associative Transcriptomics in Brassica napus

Unravelling gene expression of complex crop genomes

Contact Info

Product

Resources

About