Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping.

Abstract

Walnut shell suture strength directly impacts the ability to maintain shell integrity during harvest and processing, susceptibility to insect damage and other contamination, and the proportion of kernel halves recovered during cracking. Suture strength is therefore an important breeding objective. Here, two methods of phenotyping this trait were investigated: 1) traditional, qualitative and rather subjective scoring on an interval scale by human observers, and; 2) quantitative and continuous measurements captured by a texturometer. The aim of this work was to increase the accuracy of suture strength phenotyping and to then apply two mapping approaches, quantitative trait loci (QTL) mapping and genome wide association (GWAS) models, in order to dissect the genetic basis of the walnut suture trait. Using data collected on trees within the UC Davis Walnut Improvement Program (n = 464), the genetic correlation between the texturometer method and qualitatively scored method was high (0.826). Narrow sense heritability calculated using quantitative measurements was 0.82. A major QTL for suture strength was detected on LG05, explaining 34% of the phenotypic variation; additionally, two minor QTLs were identified on LG01 and LG11. All three QTLs were confirmed with GWAS on corresponding chromosomes. The findings reported in this study are relevant for application towards a molecular breeding program in walnut.

Plant phenotyping relevance

クルミの殻継ぎ目強度について、主観的スコアとテクスチャーアナライザーによる定量測定を比較し、表現型測定精度を向上・検証することが中心である。

Code and data availability

The paper's Data Availability statement points to a public deposit of the datasets generated and analyzed (phenotype data) at hardwoodgenomics.org, and phenotypes are also supplied in Supporting Information files. No author analysis code repository is explicitly deposited.