Development of innovative image descriptors for phenotyping peanut pod constriction and discovery of QTLs underlying this trait

doi:10.1016/j.jia.2026.02.004

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Shengzhong Zhang¹, Feifei Wang¹, Xiaohui Hu¹, Huarong Miao¹, Jun Hong², Shihua Shan¹, Xiaoyuan Chi¹, Jing Chen¹^#, Xinyou Zhang³^#

¹ Shandong Academy of Agricultural Sciences, Jinan 250100, China

² Center for Desert Agriculture, King Abdullah University of Science and Technology, Jeddah 23955, Saudi Arabia

³ Henan Academy of Agricultural Sciences, Zhengzhou 450002, China

Highlights

Novel image descriptors, along with an accurate and rapid phenotyping method, were introduced to improve pod constriction evaluation in peanut.

A major consensus QTL region spanning a 728-kb interval was newly identified for pod constriction metrics.

A candidate gene exhibiting a frameshift variation was identified within the consensus region and its diagnostic markers were developed.

Abstract
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摘要

荚果缢缩，是决定花生荚果制品商品价值及产量的关键形态性状。传统表型评价指标（如目测评分或基于果腰长度的衍生指标）存在测量精度不足或适用性有限等问题，尤其对于特殊类型的荚果测量效果不佳，限制了对该性状基因的发掘。为解决这些问题，本研究引入两种新型图像评价指标：正面与背面缢缩深度指数（Front_DI和Back_DI）。这些新型指标能够实现对不同类型荚果缢缩程度的准确、稳健评估。此外，本研究开发了基于深度学习技术的自动测量脚本，以实现上述指标的高效精准提取。本研究同时利用新型指标和传统指标对一个重组自交系群体（鲁花11号×06B16）进行表型鉴定，在三种环境中定位到4个与Front_DI相关的QTL、4个与Back_DI相关的QTL、3个与目测评分相关的QTL以及2个与果腰长度衍生指标相关QTL。在第2号染色体上检测到一个主效且不同指标共定位的QTL区域。Meta分析进一步将该区域精细定位至一个728 kb区间。在此区间内，Arahy.X14VTN基因编码区在亲本间存在一个InDel变异，导致移码突变及预测的蛋白质结构改变。针对该候选基因开发了诊断标记，并验证了其对荚果缢缩变异的遗传效应。本研究提出的新型图像评价指标与遗传位点，为阐明花生荚果缢缩性状的遗传调控机制提供了新见解，并为后续该性状的遗传改良提供了可靠工具。

Abstract

Pod constriction (PC) is a key morphological trait determining both commercial values and yield of in-shell peanuts. Conventional phenotyping metrics (visual scores and pod waist length derived descriptors) suffer from low precision or limited applicability, especially for atypical pod shapes, which have constrained discovery of underlying genes. To address these limitations, this study introduced two novel image descriptors: front and back constriction depth indices (Front_DI and Back_DI). These indices enable accurate and robust evaluation of PC across diverse pod morphologies. Additionally, a Python script employing the deep learning technology was developed to efficiently and precisely extract these metrics. By applying both novel and conventional phenotyping methods to a recombinant inbred line population (Luhua 11×06B16), this study identified four quantitative trait loci (QTLs) for Front_DI, four for Back_DI, three for visual score, and two for a pod waist length-based descriptor across three environments. A major and co-localized QTL region was consistently detected on chromosome 2. Meta-analysis further refined this region to a 728-kb consensus interval. Within this interval, an InDel was identified in the coding region of Arahy.X14VTN between the two parental lines, resulting in a frameshift mutation and a predicted alteration in protein structure. Diagnostic markers were developed for this candidate gene, confirming the genetic effect on PC variation. The novel image descriptors and genetic loci presented here improve our understanding of the genetic basis of PC in peanut and offer practical tools for molecular breeding aimed at trait improvement.

Keywords: image-based descriptor peanut pod constriction QTL candidate gene

Online: 05 February 2026

Fund:

This work was supported by the National Key Research and Development Program of China (2023YFD1202800), Natural Science Foundation of Shandong Province, the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences, Breeding Project from Department Science & Technology of Shandong Province, China (2024LZGC031), the Major Scientific and Technological Achievements Cultivation Program of Shandong Academy of Agricultural Sciences, China (CXGC2025E02), and the Taishan Scholars Program, China (tstp20240523).

About author: #Correspondence Jing Chen, E-mail: mianbaohua2008@126.com; Xinyou Zhang, E-mail: haasz@126.com

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Shengzhong Zhang, Feifei Wang, Xiaohui Hu, Huarong Miao, Jun Hong, Shihua Shan, Xiaoyuan Chi, Jing Chen, Xinyou Zhang, Shengzhong Zhang, Feifei Wang, Xiaohui Hu, Huarong Miao, Jun Hong, Shihua Shan, Xiaoyuan Chi, Jing Chen, Xinyou Zhang. 2026. Development of innovative image descriptors for phenotyping peanut pod constriction and discovery of QTLs underlying this trait. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.02.004

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