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.

Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

“…By comparison with other walnut panels used for GWAS, we observed a larger degree of fruit phenotypic variability. For instance, in the panel used in Iran, the range for nut weight was between 7.71 and 20.11 g (Arab et al, 2019), whereas in our panel, combining all the years studied, the range was between 5.22 and 22.51 g. Similarly, in the work on suture strength reported by the University of California, Davis, the use of a texture analyzer to phenotype suture strength showed a variation between 6.94 to 63.14 kg-force (i.e., between 68.06 to 619.19 N) among the 556 accessions studied (mainly from 39 biparental progenies) corresponding to a variation of 551.13 N (Sideli et al, 2020). In our walnut germplasm, with only 170 accessions and combining all the years, the variation extends from 74.40 to 776.97 N. With the high phenotypic variability and the diversity of the INRAE walnut panel used for GWAS analysis, knowing that most of these traits are highly quantitative, we may expect to find major loci involved in their variation.…”

“…For cracking related traits, using different phenotyping methods and FarmCPU model, the MTA AX-170748528 (Chr5, 13,023,760 bp) was found to be associated with the suture strength ( Sideli et al, 2020 ). This MTA was only 762 bp apart from the SNP just below the significant threshold obtained for the suture strength initial rupture.…”

“…In addition, Marrano et al (2019b) carried out a gene-mapping study to decipher the genetic control of yield, phenology, and kernel pellicle color. In addition, Sideli et al (2020) investigated the genetic control of shell suture strength phenotyped using a texture analyzer, identifying many candidate genes. By combining acquisition of accurate phenotypic data using innovative techniques with the unique walnut germplasm collection from INRAE of Bordeaux, we studied the genetic control of 25 traits related to nut quality, and we propose several candidate genes involved in those traits.…”

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

“…For the QTL mapping analysis, the ‘Idaho’ genetic map which was constructed in ( Sideli et al 2020 ) was found to have nearly a twofold increase range in map size of ‘Chandler’ genetic map. Shorter genetic maps of female parent in walnut and other species has also been observed ( Luo et al 2015 ; Kefayati et al 2019 ; Marrano et al 2019 ) thereby suggesting a lower recombination rate in the female parent of walnut.…”

“…Quantitative-trait loci mapping was performed using the genetic maps (File S5) of the bi-parental population ‘Chandler’ × ‘Idaho’ described in ( Sideli et al 2020 ). In particular, the ‘Chandler’ genetic map spanned 998.31 cM with 1,165 markers in total, while the ‘Idaho’ map contained 1,753 markers for a total length of 1,693.88 cM.…”