Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L.

Abstract

English walnut (Juglans regia L.) is an economically important crop with > 99% of US walnuts produced in California. Changes in climate and recent drought cycles have raised concerns regarding the future of nut production and responsible water use in California agriculture. Our study used an association genetics approach to characterize ecophysiological traits such as water use efficiency as estimated by carbon isotope discrimination (Δ 13 C), and photosynthetic capacity through foliar nitrogen composition, in important individuals of the Walnut Improvement Program, located at the University of California, Davis. Stable isotope and leaf measurements of 241 mature trees, representing 60 scion genotypes in established orchards were sampled in 2015 and 2016, followed by genotyping with the Walnut Axiom 700 k SNPArray. A mean Δ 13 C of 21.7‰ (σ: 0.9‰) was calculated for all individuals, as well as a mean nitrogen/leaf area (N/area) of 3.0 gN/m 2 (σ: 0.5 gN/m 2). A Bayesian analysis utilizing genomic relationships revealed rankings of the most water use efficient accessions as Solano (95-011-16), 67-013 (unreleased cross), and Tulare (67-011). 126,554 SNPs were used in a two-step association genetics approach identifying four loci associated with Δ 13 C after correction for multiple testing. Investigation of identified loci revealed an annotation on the J. regia genome of protein FAR1-related sequence 5-like, related to abiotic stress response. For uncharacterized markers, homologs were identified in Arabidopsis for two loci, similarly related to drought stress.

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

“…Recently, many marker-trait associations have been reported for different traits of interest in walnut, such as leafing date, nut-related phenotypes, and water use efficiency (Arab et al 2019; Famula et al 2019; Marrano et al 2019). We looked to see if any of these trait-associated SNPs fell within regions highly differentiated between Western and Eastern genotypes.…”

“…For the first time, it was possible to explore the gene space of Persian walnut with the prediction of 32,498 gene models, providing the basis to untangle complex phenotypic pathways, such as those responsible for the synthesis of phenolic compounds. The availability of a reference genome marked the beginning of a genomics phase in Persian walnut, allowing whole-genome resequencing (Stevens et al 2018; Zhang et al 2019), the development of high-density genotyping tools (Marrano et al 2018; Kefayati et al 2018) and the genetic dissection of important agronomical traits in walnut (Arab et al 2019; Famula et al 2019; Marrano et al 2019). However, the Chandler v1.0 assembly is highly fragmented, compromising the accuracy of gene prediction and the fulfillment of advanced genomics studies necessary to resolve many, still unanswered questions in walnut research.…”

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

“…Release of the first walnut genome sequence [30] facilitated advanced genetic and genomic studies, including development of the first high-density Axiom™ J. regia 700 K SNP genotyping array [31]. Application of this powerful genotyping tool allowed genetic dissection of crucial traits in walnut, such as nut-related traits [32] and water use efficiency [33,34]. A recent study, combining genome-wide association study (GWAS) and classical linkage mapping, found major loci for leafing and harvest dates on chromosome 1 (Chr1), and lateral fruitfulness on Chr11 [35].…”

Comparative genomics of six Juglans species reveals disease‐associated gene family contractions

“…It is anticipated that new genomic resources for Juglans (walnuts) will lead to improved timber and nut production by accelerating development of advanced agriculture, breeding efforts and resource management techniques for the genus. Already, these practices are beneficiaries of the genomic analyses and tool development potentiated by the growing pool of Juglans sequence data (Martínez‐García et al , ; Bernard et al , ; Marrano et al , ; Famula et al , ; Zhu et al , ). The recent publication of the unannotated draft reference genomes of six Juglans species: J. nigra (Eastern black walnut) , J. hindsii (Hinds black walnut) , J. microcarpa (Texas walnut) , J. sigillata (iron walnut) , J. cathayensis (Chinese walnut), J. regia (Persian or English walnut) and a member of the sister group to Juglans , Pterocarya stenoptera (Chinese wingnut), greatly expands the existing resource and provides an unprecedented opportunity to apply tools such as genomic selection to the Juglandaceae (Stevens et al , ).…”