Dissecting the genetic basis of the heterosis of Y900, an elite super-hybrid rice

sun, z.; Peng, J.; Lv, Q.; Ding, J.; Chen, S.; Duan, M.; He, Q.; wu, j.; Tian, Y.; Yu, D.; Tan, Y.; Sheng, X.; chen, j.; sun, x.; Liu, L.; Peng, R.; liu, h.; Zhou, T.; Xu, N.; Yuan, L.; wang, b.; yuan, d.

doi:10.1101/2022.07.16.500322

bioRxiv · 10.1101/2022.07.16.500322

Dissecting the genetic basis of the heterosis of Y900, an elite super-hybrid rice

sun, z.·Peng, J.·Lv, Q.·Ding, J.·Chen, S.·Duan, M.·He, Q.·wu, j.·Tian, Y.·Yu, D.·Tan, Y.·Sheng, X.·chen, j.·sun, x.·Liu, L.·Peng, R.·liu, h.·Zhou, T.·Xu, N.·Yuan, L.·wang, b.·yuan, d.

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Abstract

Y900 is one of the top hybrid rice varieties with a yield exceeding 15 t/hm2. To dissect the mechanism of heterosis, the male parent line R900 and female parent line Y58S were sequenced using long-read and Hi-C technology. High-quality reference genomes of sizes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 SNPs and 299,149 Indels. No megabase level structural variations exist. >75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the Geng/japonica-type genetic components from different male parents showed an increasing trend from phase 2-4 super-hybrid rice; Transcriptome analysis revealed that additive and dominance effects are the main genetic effects that constitute the heterosis of Y900. Allele-specific expression patterns and expression regulation patterns are quite dynamic in different tissues. For young panicle tissues, cis-regulation is dominant, while trans-regulation is more popular in leaf issues. Overdominance is more likely regulated by the trans-regulation mechanism. The differential gene expression and regulation pattern are closely related to Geng/japonica introgression. Additionally, R900 contained several excellent japonica haplotypes, such as NAL1, OsSPL13, Ghd8, OsBRI1, and DTH2, which make a good complement to Y58S. The fine tune mechanism through dynamic expression or regulation pattern change, especially on some key functional genes, is the base for heterosis.

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sun, z., Peng, J., Lv, Q., Ding, J., Chen, S., Duan, M., He, Q., wu, j., Tian, Y., Yu, D., Tan, Y., Sheng, X., chen, j., sun, x., Liu, L., Peng, R., liu, h., Zhou, T., Xu, N., Yuan, L., wang, b., yuan, d.. 2022-07-17. Dissecting the genetic basis of the heterosis of Y900, an elite super-hybrid rice. https://doi.org/10.1101/2022.07.16.500322

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