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

Jiayu Yao; Shaolian Jiang; Hu Li; Qin Li; Zhaowei Qiu; Aifen Tao; Pingping Fang; Jiantang Xu; Lihui Lin; Jianmin Qi; Liwu Zhang

doi:10.1007/s11032-023-01435-8

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

Mol Breed. 2023 Nov 24;43(12):85. doi: 10.1007/s11032-023-01435-8. eCollection 2023 Dec.

Authors

Jiayu Yao^{1

2}, Shaolian Jiang^{1

2}, Hu Li^{1

2}, Qin Li^{1

2}, Zhaowei Qiu^{1

2}, Aifen Tao^{1

2}, Pingping Fang^{1

2}, Jiantang Xu^{1

2}, Lihui Lin^{1

2}, Jianmin Qi^{1

2}, Liwu Zhang^{1

2}

Affiliations

¹ Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
² Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.

PMID: 38009098
PMCID: PMC10667207 (available on 2024-11-24)
DOI: 10.1007/s11032-023-01435-8

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.

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