Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus)

Yuting Yang; Wenxiang Wang; Qiong Hu; Harsh Raman; Jia Liu

doi:10.3389/fpls.2022.1097534

Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus)

Front Plant Sci. 2023 Jan 13:13:1097534. doi: 10.3389/fpls.2022.1097534. eCollection 2022.

Authors

Yuting Yang^{1

2}, Wenxiang Wang^{1

3}, Qiong Hu^{1

3}, Harsh Raman⁴, Jia Liu^{1

3}

Affiliations

¹ Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.
² Shenzhen Graduate School, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
³ Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
⁴ New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia.

Abstract

Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.

Keywords: GWAS; RNA-seq; candidate genes; pod orientation; rapeseed.

Grants and funding

This work was supported by the Natural Science Foundation of China (U19A2029), the Central Public-interest Scientific Institution Basal Research Fund (No. 161017202203 and 1610172020001) and an open project (KF2020007) of the Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P. R. China. We thank the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences for computational and experimental support. We also thank Grains Research and Development Corporation for supporting collaborative research carried out at NSW DPI and OCRI, Wuhan, under the DAN00208 project.