Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Abstract

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

Transcriptomic analysis of rapeseed (Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas

“…Both direct yield component traits and indirect yield-related traits are elaborately controlled by several genes and are highly influenced by environmental conditions ( Van Camp, 2005 ; Shi et al, 2009 ; Ding et al, 2012 ; Zhao et al, 2016 ; Lu et al, 2017 ). The identification of yield candidate genes implies the detection of important genes for agricultural and economic quantitative traits ( Raboanatahiry et al, 2018 , 2022 ; Hu et al, 2021 , 2022 ; Pal et al, 2021 ; Zheng et al, 2022 ). In the model plant Arabidopsis thaliana , 425 genes were collected from the TAIR website 2 to be related to flowering time, plant height, branch number, seed number, seed weight, and SY ( Shi et al, 2009 ).…”

“…Then, 147 SY-related, 189 SW-related, and 28 PN-related Brassica napus homologous genes of Arabidopsis thaliana yield-related genes were found ( Raboanatahiry et al, 2018 ). Based on the construction of a quantitative genomic map of Brassica napus , Raboanatahiry further revealed 517 regions of overlapping QTLs that harbored 2,744 candidate genes and might affect multiple traits simultaneously ( Raboanatahiry et al, 2022 ). Hu unraveled the genomic basis for the selection of adaptation and agronomic traits and identified 628 associated locus-related causative candidate genes for 56 agronomically important traits (including plant architecture and yield traits) through genome-wide association studies ( Hu et al, 2022 ).…”

Linkage and association mapping of ovule number per ovary (ON) in oilseed rape (Brassica napus L.)

“…To assess whether the QTLs detected in the present study are in the genomic regions important for oilseed rape breeding, we compared the physical interval of our QTLs with the previously reported QTLs. The comparison was restricted to SY-related traits only, like seed number (SN), the number of silique/pods (NP) and seed weight (SW) in different mapping populations following Raboanatahiry et al (Raboanatahiry et al 2018(Raboanatahiry et al , 2022. We searched the previously published QTLs within the physical interval of the QTLs detected in our study (Table 1).…”

“…To date, nearly hundred QTLs related seed number (SN) were identi ed in rapeseed (Zhu et al 2020;Raboanatahiry et al 2022); among these, qSS.C9 (BnaC9.SMG7b) is the only SN-related QTL cloned to date (Li et al 2015). By contrast, the genetics of ON remains largely unexplored and only few QTLs related to ON were revealed (Khan et al 2019;Qadir et al 2022) via GWAS.…”

“…The role of auxins and cytokinin and their crosstalk in ovule initiation and development is well elucidated in Arabidopsis(Galbiati et al 2013;Cucinotta et al 2016). Functional analysis of these gene in oilseed rape will open up new ways towards the understanding molecular mechanism of ovule development and number determination.In B napus, 2,438 QTLs have been identi ed for 79 yield-related traits(Raboanatahiry et al 2022). Several of these identi ed QTLs overlap or coincides with each other.…”