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

Abstract

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

Different rates of pollen and seed gene flow cause branch‐length and geographic cytonuclear discordance within Asian butternuts

“…Taken together, the two genes are under positive selection are in J. mandshurica , but not in J. cathayensis . JMA026091 is a TVP38/TMEM64 family membrane protein encoding genes linked with the shell thickness of walnut in J. regia (Bernard et al ., 2021). The function of JMA025840 is unknown but, considering it is adjacent to JMA026091, we suspected that JMA025840 is actually under linked selection.…”

“…4). One of the two genes under selection is a TVP38/TMEM64 family membrane protein encoding gene, which may link with the shell thickness of walnut (Bernard et al ., 2021). The pattern of selection is consistent with the result of IBE analysis in which genetic distance is not associated with environmental distance (Fig.…”

Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication

“…The nuts of both wild and cultivated Persian walnut are gathered and consumed [ 24 , 25 ], but wild trees produce smaller fruits (2–3 cm in diameter) with thicker shells, while domesticated varieties have larger fruits (3–6 cm in diameter) with thinner shells [ 26 ]. A genomic study of Iranian walnuts was able to link a SNP on chromosome 13 to shell thickness [ 27 ], and two other studies have reported candidate genes for shell thickness [ 28 , 29 ]. These inferences became possible with the release of the first walnut reference genome, Chandler v1.0 [ 30 ], which allowed whole-genome resequencing [ 29 , 31 , 32 ], the development of high-density genotyping tools [ 33 ], and the genetic dissection of agronomical traits in walnut, including the mentioned shell thickness [ 27 , 28 , 34 – 36 ].…”

“…A genomic study of Iranian walnuts was able to link a SNP on chromosome 13 to shell thickness [ 27 ], and two other studies have reported candidate genes for shell thickness [ 28 , 29 ]. These inferences became possible with the release of the first walnut reference genome, Chandler v1.0 [ 30 ], which allowed whole-genome resequencing [ 29 , 31 , 32 ], the development of high-density genotyping tools [ 33 ], and the genetic dissection of agronomical traits in walnut, including the mentioned shell thickness [ 27 , 28 , 34 – 36 ]. Chromosome-level assemblies are now available for both J. regia and J. sigillata , the latter a close relative endemic in Guizhou, Sichuan, Southeast Xizang (Tibet), Yunnan, Bhutan, and Sikkim where its wood and nuts are used similarly to those of Persian walnut [ 37 ].…”

Multi‐environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection

“…Transcription factors from the BEL1-LIKE HOMEODO-MAIN (BLH) family were found to interact with OFPs in Arabidopsis, cotton, rice, and banana (Hackbusch et al, 2005;Li et al, 2011;Liu & Douglas, 2015;Pagnussat et al, 2007;Schmitz et al, 2015;Wang et al, 2016;Zhang et al, 2016). Moreover, Bernard et al (2021) found that a BLH protein was likely associated with walnut kernel weight. A homolog of BEL1-LIKE HOMEODOMAIN PROTEIN 2 (BLH2) underlying the QTL FWe-P2.4, detected with the strongest marker-FWe association, may thus affect fruit weight.…”