Identification of Sex Determination Molecular Marker Based on Genome-wide Association Study of Idesia polycarpa

doi:10.11983/CBB24029

Abstract

Abstract: INTRODUCTION Sexual differentiation of plants, as known as dioecy, is the phenomenon of sexually dimorphic traits, which means that the female and male reproductive organs are on different individuals. In agronomic or economic ap- plications, dioecy is not a desired character for various reasons. Therefore, a simple and effective method for distin- guishing female and male individuals is a common goal for the people in many fields. As so far, molecular marker is a gold standard for sex identification genetically. It is necessary to develop a molecular technique to detect sexual systems in the dioecious plants. RATIONALEIn plants, the origin and evolution of sex chromosomes was independent in many species, therefore sex determination region/chromosome was different among them. Idesia polycarpa is a deciduous tree, making it an attrac- tive model system with which to study sex determination mechanism. We characterized the re-sequence data of female and male individuals from natural population. We used these data to identify the sex determination systems by statistics unique sequences in females and males. To detect the sex chromosome, we analysed the single nucleotide polymor- phisms (SNPs) by genome-wide association study (GWAS). RESULTSThe information of genome contains the secret code of various traits, so we mined the re-sequenced data of females and males. We calculated the common and unique reads in females and males, compared the unique reads between them, and found that the unique reads of females were much more than that of males. The result suggested that the sex determination system of I. polycarpa was ZW/ZZ. We then identified 30 million high quality SNPs in the population by mapping to the reference genome, calculated the p value of each SNP, drew a Manhattan plot. The result showed the highest peak on the end of 19 chromosome. We analysed the heterozygote of SNPs in this peak, and the result showed that the SNPs were heterozygotic in females, but homozygotic in males. The result confirmed that the sex determination system in I. polycarpa is ZW/ZZ. Further, a cleave amplified polymorphic sequences (CAPS) mo- lecular marker was developed according to the significant SNPs, and was successfully applied to different female and male individuals. CONCLUSION In the Salicaceae family, there were two kinds of sex determination system, one is XX/XY (females are homogametic XX, and males are heterogametic XY), another is ZW/ZZ (females are heterogametic ZW, and males are homogametic ZZ). At present, most studies on the sex-determining regions and genes in the Salicaceae family are carried out by methods such as genome, transcriptome, and resequencing analyses. Our results showed that the sex determination system in I. polycarpawas ZW/ZZ, and the 19^th chromosome is most likely associated with sex determination. And a CAPS molecular marker was developed, which is a simple and fast method for efficient identification sex at seedling stage. The research provided a useful way to the planting pattern of I. polycarpa.

Identification of sex determination molecular marker of Idesia polycarpa. Trees of I. polycarpa are indistinguishable as to sex without examination of the flowers. A CAPS molecular marker was developed based on genome wide analysis study on a natural population.

Key words: Idesia polycarpa, sex determination, molecular marker

Yi Zuo, Hongbing Liu, Zhigang Yang, Bin Li, Haoxin Xiang, Chunzhen Zhu, Lei Wang. Identification of Sex Determination Molecular Marker Based on Genome-wide Association Study of Idesia polycarpa[J]. Chinese Bulletin of Botany, 2024, 59(3): 414-421.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24029

https://www.chinbullbotany.com/EN/Y2024/V59/I3/414

Figures/Tables 5

Figure 1 The sex-determination system in Idesia polycarpa (A) Distribution of sex-specific K-mers (MSK: Male-specific K-mers; MBK: Male-biased K-mers; FSK: Female-specific K-mers; FBK: Female-biased K-mers.). (B) The histogram shows the quantitative differences between MSK and FSK.

Figure 2 The SNPs distribution on reference genome between male and female groups

The red arrow indicates the significant peak.

Homo: Homozygous; Heter: Heterozygous

Figure 5 The cleaved amplified polymorphic sequences (CAPS) marker and agarose gel electrophoresis were applied for sex determination (A) The sequence difference can be recognized by specific restriction enzyme between male and female; (B) The fragment difference was determined by agarose gel electrophoresis. The unique band of 375 bp was associated with male, while the three bands (375 bp, 195 bp and 180 bp) were associated with female. M: DNA marker. The DNA ladder measures from 600 bp to 100 bp.

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