Transcriptomics‐assisted quantitative trait locus fine mapping for the rapid identification of a nodulin 26‐like intrinsic protein gene regulating boron efficiency in allotetraploid rapeseed

Abstract

Allotetraploid rapeseed (Brassica napus L., An An Cn Cn , 2n = 4x = 38) is extraordinarily susceptible to boron (B) deficiency, a ubiquitous problem causing severe losses in seed yield. The breeding of B-efficient rapeseed germ plasm is a cost-effective and environmentally friendly strategy for the agricultural industry; however, genes regulating B efficiency in allotetraploid rapeseed have not yet been isolated. In this research, quantitative trait locus (QTL) fine mapping and digital gene expression (DGE) profiling were combined to identify the candidate genes underlying the major-effect QTL qBEC-A3a, which regulates B efficiency. Comparative phenotype analyses of the near-isogenic lines (NILs) indicated that qBEC-A3a plays a significant role in improving B efficiency under B deficiency. Exploiting QTL fine mapping and DGE analyses revealed a nodulin 26-like intrinsic protein (NIP) gene, which encodes a likely boric acid channel. The gene co-expression network for putative B transporters also highlighted its central role in the efficiency of B uptake. An integration of whole-genome re-sequencing (WGS) with bulked segregant analysis (BSA) authenticated the emerging availability of QTL-seq for the QTL analyses in allotetraploid rapeseed. Transcriptomics-assisted QTL mapping and comparative genomics provided novel insights into the rapid identification of quantitative trait genes (QTGs) in plant species with complex genomes.

Discovery of genomic regions and candidate genes controlling shelling percentage using QTL‐seq approach in cultivated peanut (Arachis hypogaea L.)

“…According to the QTL‐seq approach, only one parent was sequenced and used as reference to compare the two extreme bulks (Takagi et al ., ), and recent reports in cucumber (Lu et al ., ), tomato (Illa‐Berenguer et al ., ), rapeseed (Hua et al ., ), chickpea (Singh et al ., ), pigeonpea (Singh et al ., ), peanut (Pandey et al ., ), soybean (Zhong et al ., ) and rice (Wambugu et al ., ) used one parent as reference. Whether the choice of different parent would affect the results were not reported.…”

“…This approach is cost‐effective as sample number is less for sequencing and facilitates development of cost‐effective markers in less time for deployment in GAB. This approach has been deployed in several crops including rice (Wambugu et al ., ), cucumber (Lu et al ., ), tomato (Illa‐Berenguer et al ., ), rapeseed (Hua et al ., ), chickpea (Singh et al ., ), pigeonpea (Singh et al ., ), peanut (Pandey et al ., ) and soybean (Zhong et al ., ), and proved to be very successful in RIL populations with phenotyping data generated in multiple environments. Since the reference genome sequence of cultivated peanut is still unpublished, the available reference genome sequences of its two diploid ancestors, A. duranensis (AA, 2 n = 2 x = 20) and A. ipaensis (BB, 2 n = 2 x = 20) (Bertioli et al ., ) provided a foundation to find candidate genes and SNPs present in QTL regions.…”

Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus

“…Single gene mutations may affect the expression of some genes in the common metabolic network. Consequently, further identification of the network is necessary, and simultaneously the rapid capture of causal genes requires the use of transcription and fine mapping methods50.…”

A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus

“…Combining GWAS and RNA-seq can provide both the power and resolution needed to identify DE candidate genes, and has proven to be more successful than either strategy alone3839. Based on integrative analyses of RNA-seq and GWAS in B. napus , 8 and 24 candidate genes putatively associated with drought tolerance and stem resistance to Sclerotinia sclerotiorum , respectively, were identified3840.…”

“…Based on integrative analyses of RNA-seq and GWAS in B. napus , 8 and 24 candidate genes putatively associated with drought tolerance and stem resistance to Sclerotinia sclerotiorum , respectively, were identified3840. More recently, QTL fine mapping, digital gene expression (DGE) profiling, and whole-genome re-sequencing (WGS) were combined to identify a NODULIN 26-LIKE INTRINSIC PROTEIN gene involved in regulating boron uptake efficiency in B. napus 39. Applying a similar strategy, we identified 73 TFs and 174 genes that were DE in at least one tissue from a total of 1113 genes within the LD blocks of 21 significant SNPs that associated with more than one trait.…”