# Genome‐wide identification of quantitative trait nucleotides for plant architecture‐related traits in peanut

## TL;DR

This study identifies genetic markers in peanuts that influence plant structure traits, which could help improve yield and resilience.

## Contribution

The discovery of novel genomic regions and SNPs associated with peanut architecture traits, including a new region for stem diameter.

## Key findings

- A novel genomic region on Arahy.03 was associated with stem diameter for the first time.
- Two SNPs on Arahy.09 were identified as potential diagnostic markers for MSH and FBL.
- An SNP on Arahy.05 was linked to MSH, FBL, and NSK and is near a protein kinase superfamily gene.

## Abstract

Peanut (Arachis hypogaea L.) is globally recognized as an important oilseed crop. Traits related to plant architecture are closely associated with yield in peanut. In this study, we focused on four specific traits related to plant architecture—first branch length (FBL), main stem height (MSH), stem diameter (SD), and the number of nodes on the main stem (NSK)—across three locations. Using whole‐genome resequencing data from a genetically diverse collection of peanut landraces, we conducted a genome‐wide association study analysis to identify genetic variants associated with these traits. Notably, a novel genomic region on Arahy.03:39916768–42652757 was associated with SD for the first time. Homology analysis suggested that two annotated genes within this region may contribute to stem elongation and seed development. For MSH, NSK, and FBL, more than half of the significantly associated single‐nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05. Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL: one homologous gene near these SNPs encoded an E3 ubiquitin–protein ligase, while the other encodes cinnamyl alcohol dehydrogenase. Additionally, one SNP at Arahy.05:53493734 was identified as a potential diagnostic marker for MSH, FBL, and NSK and validated using the penta‐primer amplification refractory mutation system and quantitative real‐time polymerase chain reaction. A gene near this SNP belongs to the protein kinase superfamily. Enzymes are known to regulate diverse cellular and biological processes, including plant development. These findings advance our understanding of the genetic basis of peanut architecture and provide valuable markers for future yield improvement efforts.

We identified 411 significant single‐nucleotide polymorphisms (SNPs) associated with four traits related to peanut architecture through a genome‐wide association study.For the trait of stem diameter, we identified a novel genomic region on Arahy.03:39916768–42652757, associated with this trait for the first time.Two SNPs located at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for main stem height (MSH) and first branch length (FBL).An SNP located at Arahy.05:53493734 was associated with MSH, FBL, and the number of nodes on the main stem. The genomic region surrounding this SNP has been annotated as part of the protein kinase superfamily, which plays a crucial role in plant development.

We identified 411 significant single‐nucleotide polymorphisms (SNPs) associated with four traits related to peanut architecture through a genome‐wide association study.

For the trait of stem diameter, we identified a novel genomic region on Arahy.03:39916768–42652757, associated with this trait for the first time.

Two SNPs located at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for main stem height (MSH) and first branch length (FBL).

An SNP located at Arahy.05:53493734 was associated with MSH, FBL, and the number of nodes on the main stem. The genomic region surrounding this SNP has been annotated as part of the protein kinase superfamily, which plays a crucial role in plant development.

The yield of peanut (Arachis hypogaea L.) is closely linked to its structural characteristics, which can significantly influence planting density and lodging resistance. Here, we examined the complete genomic sequence of the peanut to identify minor variations that may correlate with peanut architecture. We specifically analyzed the genome to uncover insights related to four specific traits: first branch length (FBL), main stem height (MSH), SD, and number of nodes on the main stem. Notably, some of these loci were associated with multiple traits, particularly MSH and FBL, corroborating findings from previous studies. One of our most exciting discoveries was three genomic loci that may serve as a reliable predictor for plant architecture. Furthermore, we identified a crucial segment and two candidate genes on Arahy.03 that appear to be linked to stem thickness. Gaining insights into these genomic loci could prove invaluable for enhancing the cultivation of more robust and productive peanut plants in the future.