Genetic Analysis of Walnut (Juglans regia L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform

Abstract

Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation. Progeny from both a bi-parental population of 168 trees ('Chandler' × 'Idaho') and a genome-wide association (GWAS) with 528 trees of the UC Davis Walnut Improvement Program were analyzed. Color phenotypes were found to have overlapping regions in the 'Chandler' genetic map on Chr01 suggesting complex genetic control. In the GWAS population, multiple, small effect QTLs across Chr01, Chr07, Chr08, Chr09, Chr10, Chr12 and Chr13 were discovered. Marker trait associations were co-localized with QTL mapping on Chr01, Chr10, Chr14, and Chr16. Putative candidate genes controlling walnut pellicle pigmentation were postulated.

Applying molecular and genetic methods to trees and their fungal communities

“…Genome-wide sequencing methods including whole genome resequencing are gaining importance in QTL mapping in trees (Marinoni et al 2020). While the generation of genomic data is no longer a limiting factor for some model tree species, additional efforts are needed in high precision and high throughput phenotyping to dissect the genetic basis of complex phenotypic traits (Sideli et al 2020;Virlet et al 2015). Also, allelic variation in the crossing parents and the comparatively low resolution of the QTL mapping approach limits the detection of genes underlying trait-specific QTLs, high precision mapping resulting in QTL regions that still contain several hundred genes (Bdeir et al 2017).…”

Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars

“…Its medicinal efficacy is mostly related to the rich polyphenol and flavonoid components, which have antioxidant and immunity-enhancing effects, and has been a hotspot for research and development in recent years [ 26 – 28 ]. The walnut kernel consists of the embryo (seed kernel or kernel) and the endopleura (seed coat, kernel membrane), the walnut endopleura is wrapped in a layer of film on the surface of the kernel [ 29 , 30 ]. Within the walnut fruit shell, the kernel is surrounded by a protective tan-brown skin referred to as the endopleura.…”

Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut (Juglans regia L.)

“…There is clinical evidence that walnuts can prevent coronary heart disease and promote cardiovascular health [4], and these benefits are closely related to the fact that walnuts are abundant in polyphenols, especially flavonoids. Common walnuts have green leaves and husks and light yellow to brown seed coats [5], but the 'Zijing' walnut variety currently found in Beijing, China, has purplish-red branches, leaves, flowers, husks, and seed coats and is rich in anthocyanins [6]. Walnut color is one of the key attributes that promote walnut sales and cater to consumer preferences [7], and walnuts with a purplish-red seed coat are favored by consumers for their rich anthocyanin content.…”