# Genetic analysis of silique and seed traits in Brassica juncea (L.) Czern. under differential doses of nitrogen application

## TL;DR

This study explores how nitrogen levels affect silique and seed traits in mustard, identifying genes that could help improve breeding through marker-assisted selection.

## Contribution

The study identifies 16 key genes associated with silique and seed traits in mustard under varying nitrogen levels.

## Key findings

- Genotype × nitrogen interactions significantly affect silique length, seeds per silique, and rupture energy.
- RNA-seq data revealed expression-level variations for candidate genes like SHP2 and BG4.
- The study provides insights for marker-assisted selection in mustard breeding.

## Abstract

Mustard, a major source of edible and industrial grade oils in the Indian subcontinent and various regions of Australia, Eastern Europe, and Canada, is also a protein resource for the animal feed industry. Silique and seed size are key traits for mustard improvement, but their inheritance mechanisms are not fully understood. We evaluated 92 inbred lines for silique length, seeds per silique, seed size, and rupture energy required to shatter a pod at three levels of nitrogen application in two crop seasons. Genotypes showed large phenotypic variations and a continuous distribution for all silique-related traits, suggesting a quantitative inheritance. Genotype × nitrogen interactions were significant for silique length, seeds per silique, and rupture energy. Association analysis identified 59 significant SNPs, whose annotations facilitated the prediction of 16 important genes underlying observed phenotypic variations. These genes are associated with silique formation (SHP2), grain formation (BG1, BG4), cell elongation (BRI1), grain filling (AT1G12500, AT1G77610, SWEET1, and AT3G14410), and silique shattering (UBP15, CO, INDEHISCENT, AGAMOUS1, FRUITFULL, and SHP2). RNA-seq data from 18 mustard genotypes revealed expression-level variations for identified candidate genes. Upregulation of SHP2 for SPS and resistance to silique shattering was observed, while downregulation of BG4 was observed in two genotypes with smallest seeds. This study provides valuable insight that may facilitate the marker-assisted selection (MAS) breeding for silique traits.

The online version contains supplementary material available at 10.1038/s41598-025-07758-0.