Genome-wide association study reveals loci and candidate genes of flowering time in jute (Corchorus L.)

Abstract

Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. β-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01435-8.

Keywords: CcPRR7; Flowering time; GWAS; Jute.

Fig. 1

Genome-wide association analysis of flowering time in 242 jute accessions, with Manhattan plot on the left and Q-Q plot on the right. The dashed line of the Manhattan plot represents the significance threshold. a GLM model in 2021. b FaST-LMM model in 2021. c GLM model in 2022. d FaST-LMM model in 2022

Fig. 2

Association mapping of flowering time in jute. The upper part is the Manhattan plot of overlapping intervals, and the bottom is the LD heatmap. The dashed lines indicate the candidate region of the peak. a Chromosome 1: 10.22–13.19 Mb. b Chromosome 3: 5.45–6.25 Mb. c Chromosome 4: 14.59–15.45 Mb. d Chromosome 4: 52.90–56.69 Mb. e Chromosome 5: 41.86–43.35 Mb. f Chromosome 7: 45.94–46.22 Mb

Fig. 3

Potential breeding value of different genotypes for significant loci of flowering time in 242 jute varieties. a Flowering time in different genotypes. 21FT means flowering time in 2021. 22FT means flowering time in 2022. b Plant height in different genotypes. 21FT means plant height in 2021. 22FT means plant height in 2022

Fig. 4

Functional identification of the major gene CcPRR7. a The neighbor-joining phylogenetic tree of CcPRR7 and its orthologs from monocotyledon and dicotyledon. b Schematic of CcPRR7 overexpression vector construction. c Detection of transgenic Arabidopsis lines on the transcriptional level. ***P < 0.001. d Expression analysis of photoperiod-related genes in CcPRR7 overexpression lines. ***P < 0.001

Fig. 5

Haplotype and promoter activity analysis of CcPRR7. a The gene structure of CcPRR7 and the loci information of 3 SNPs. Hap: haplotype. Hap.1: haplotype 1. Hap.2: haplotype 2. Hap.3: haplotype 3. b SNP variation of CcPRR7 in Huangma179 (Hap.2) and Aidianyehuangma (Hap.3). c Boxplots indicate phenotypic differences in flowering time corresponding to SNP (3_5544750) alleles in Corchorus capsularis populations, **P < 0.01. d Genotyping of CcPRR7 in a population of recombinant inbred lines by Kompetitive Allele Specific PCR (KASP). Blue and red points represent two homozygous genotypes, green points represent the parental complementary genotype, and black squares represent non-template control (NTC). e. Expression level analysis of CcPRR7 under short-day and long-day conditions, reference gene: Cc18SrRNA, **P < 0.01. f β-glucuronidase activity assay of CcPRR7 promoter in Meifeng4 (Hap.2) and Aidianyehuangma (Hap.3). g Luciferase activity assay of CcPRR7 promoter in Meifeng4 (Hap.2) and Aidianyehuangma (Hap.3)

Fig. 6

Expression analysis of photoperiod co-responsive genes in Huangma179 under different photoperiodic treatments. a Phenotypic analysis of Huangma179 flowering time under short-day treatment, ***P < 0.001. b Venn diagram of differentially expressed genes in Huangma179 under different photoperiod treatments. CK: sample without photoperiod treatment. S15d: sample treated with short-day for 15 days. L15d: sample treated with long-day for 15 days. c Relative expression analysis of DEGs involved in photoperiodic pathway