Genome‐wide association studies of fruit quality traits in jujube germplasm collections using genotyping‐by‐sequencing

Abstract

Chinese jujube (Ziziphus jujuba Mill.) is an important fruit crop and harbors many highly diverse traits of potential economic importance. Fruit size, stone size, and fruit cracking have an important influence on the commercial value of jujube. This study is the first to conduct a genome-wide association study (GWAS) on 180 accessions of jujube and focuses on locating single-nucleotide polymorphisms (SNPs) associated with nine important fruit quality traits. Genotyping was performed using genotyping-by-sequencing and 4651 high-quality SNPs were identified. A genetic diversity analysis revealed the presence of three distinct groups, and rapid linkage disequilibrium decay was observed in this jujube population. Using a mixed linear model, a total of 45 significant SNPtrait associations were detected, among which 33 SNPs had associations with fruit size-related traits, nine were associated with stone size-related traits, and three with fruit cracking-related traits. In total, 21 candidate genes involved in cell expansion, abiotic stress responses, hormone signaling, and growth development were identified from the genome sequences of jujube. These results are useful as basic data for GWAS of other jujube traits, and these significant SNP loci and candidate genes should aid marker-assisted breeding and genomic selection of improved jujube cultivars.

Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

“…For this investigation, we successfully applied GBS technology to generate high-quality SNPs across four Ziziphus species. The number of SNPs generated in our study (10,889) is higher than in many similar studies, including the previously reported 4,680 SNPs from GBS in a 150 member Z. jujuba core collection (Chen et al 2017) and the 4,651 SNPs found in the extended, 180-accession Z. jujuba panel (Hou et al 2020). This suggests, not only that GBS and reference sequence-based alignment is an efficient approach for SNPs identification in related Ziziphus species, but also that the addition of accessions from different species and origins allowed us to capture previously untapped molecular diversity that could prove valuable for marker-assisted approaches to both conservation and breeding.…”

“…Although the markers identified can be used for markerassisted selection, further work would be required to validate any candidate genes. Nonetheless, to the best of our knowledge, the MTAs identified in this study were novel (although some similar fruit traits were studied using GWAS by Hou et al (2020) in Z. jujuba) and they had high allelic effects. Utilizing the different species and origins resulted in a wide range of trait phenotypes for the majority of traits that allowed us to explore novel genetic associations.…”

“…GBS has been successfully used in many crop species including maize, barley, wheat, rice (Poland and Rife, 2012) and, recently, in Z. jujuba Mill. for molecular markers discovery in a core collection (Chen et al 2017) and for GWAS of domestication and fruit traits (Gou et al, 2020;Guo et al, 2021;Hou et al 2020). Molecular markers for any identified quantitative trait loci (QTL) can then be used for marker-assisted selection in plant breeding programs (He et al 2014) to incorporate alleles from diverse, genetic resources.…”

Comparative Transcriptomic Analyses of Different Jujube Cultivars Reveal the Co-Regulation of Multiple Pathways during Fruit Cracking

“…To the best of our knowledge, a few studies have investigated the molecular basis of jujube fruit cracking. A recent study detected three SNPs that were significantly associated with the fruit cracking-related traits of jujube germplasm collections by means of association mapping [ 17 ]. Using RNA-seq technology, Liu et al [ 18 ] profiled the DEGs between cracked and normal ‘Huping’ jujube fruits.…”

“…We have studied jujube breeding for a long time and have specifically focused on fruit cracking and have observed the continuous fruit cracking of 150 jujube cultivars in the core collection for many years. Based on previous research, the cracking-susceptible cultivars ‘Cuizaohong’ and ‘Jinsixiaozao’ and the cracking-resistant cultivar ‘Muzao’ were selected to study the molecular mechanisms that are associated with cracking [ 17 , 19 ]. In this study, we compared the transcriptomes of the half-red fruits from cracking ‘Cuizaohong’ (CC), non-cracking ‘Cuizaohong’ (NC), cracking ‘Jinsixiaozao’ (CJ), non-cracking ‘Jinsixiaozao’ (NJ), and non-cracking ‘Muzao’ (NM) using RNA-seq analysis.…”