Genome-Wide Analysis and Polymorphism Evaluation of Microsatellites Involved in Photoperiodic Flowering-time Genes in Kenaf (Hibiscus Cannabinus L.)

ABSTRACT

Kenaf (Hibiscus cannabinus L.) is one of the most important crops, which is grown for natural fiber production. However, the deficiency of SSR markers limits the genetic improvement of kenaf. In this study, SSRs (simple sequence repeats) were identified from the reference genome and coding sequence (CDS) of Fuhong952, a sequenced variety of kenaf. SSR loci were mined using the Seiners 2.0 software and the characteristics of SSR loci were analyzed. A total of 301, 505 and 14, 269 SSRs with an overall density of 279.70 SSRs/Mb and 182.70 SSRs/Mb were identified from whole-genome and CDS, respectively. 12bp was the predominant repeat in the entire genome and CDS, trinucleotide repeats were the most abundant among both types of sequences. For different SSR repeat types, the SSR frequency decreased dramatically as repeat times increased. AT was the most frequent single motif across the entire genome, while AG was the most abundant motif in CDS. The homologous genes in kenaf were obtained from the 71 genes associated with photoperiodic flowering-time. As such, 115 primer pairs were designed and synthesized using these homologous genes in kenaf. The amplification of 108 pairs revealed stable and clear bands, and two pair of primers located in HcFCA and HcVIN3 were significantly associated with photoperiodic flowering-time using one-way ANOVA and regression analysis. The detailed results of the SSR markers in this study provides valuable information about the frequency distribution of SSRs in the whole genome and will expedite genomic research for improvement in kenaf.

摘要

红麻是生产天然纤维的重要作物之一。然而, SSR标记的缺乏限制了红麻的遗传改良。本研究从红麻品种福红952的参考基因组和编码序列 (CDS) 中鉴定SSR (simple sequence repeats) 。利用seiners2.0软件挖掘SSR位点, 分析SSR位点特征。全基因组和CDS分别鉴定出301, 505和14, 269个SSR, 总密度分别为279.70 SSRs/Mb和182.70 SSRs/Mb。12bp大小的重复序列和三核苷酸重复序列是全基因组和CDS中最多的重复序列类型。对于不同的SSR重复类型, 随着重复次数的增加, SSR频率急剧下降。AT是全基因组中最常见的基序, AG是CDS中最丰富的基序。利用拟南芥71个光周期开花时间相关的基因鉴定红麻同源基因, 并设计合成了115对引物, 其中108对引物能稳定扩增出清晰的条带。单因素方差分析和回归分析表明HcFCA和HcVIN3两对引物与光周期开花时间显著相关。对红麻SSR标记的详细研究为红麻基因组中SSR的频率分布提供了有价值的信息, 并将加速红麻改良的基因组研究。

KEYWORDS:

• Kenaf (Hibiscus cannabinus L)
• Genome
• SSR markers
• Genetic diversity
• Flowering-time

关键词:

• 红麻
• 基因组
• SSR标记
• 遗传多样性
• 开花期

Author’s contribution

LZ has designed and supervised experiments. YX and LZ helped to prepare the reagents and materials. YX, YL, CW, and MZA participated in the editing and revision of the manuscript. YX and DL carried out the data analysis and wrote the paper. JQ and LZ contributed to new germplasm and techniques. All authors read and approved the final manuscript.

Availability of data and material

The genome and CDS of kenaf from NGDC (https://bigd.big.ac.cn/gwh) public database (Accession number: GWHACDB00000000)

Code availability

Not Applicable

Consent to participate

All authors read and approved the final manuscript.

Consent to publication

All authors approved the publishing of manuscript.

Disclosure Statement

The authors declare that they have no conflict of interest.

Ethics approval

Not Applicable

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (31972968); the National Agri-Industry Technology Research System for Crops of Bast and Leaf Fiber, China (nycytx-19-E06).