Hongbo Pang

Plant height is an important agronomic trait in rice and shows marked divergence between wild and cultivated germplasm. To identify loci associated with plant height variation from wild rice, we developed a BC ₄ F ₇ chromosome segment substitution line population of 308 lines derived from Yuanjiang common wild rice ( Oryza rufipogon ) and elite cultivar Youzhan 8 ( Oryza sativa ). Bulked segregant analysis coupled with sequencing identified a 13.6‐Mb quantitative trait loci region on chromosome 7 associated with plant height. Eight prioritized candidate genes were identified within this interval based on sequence polymorphism and functional annotation, including known regulators OsTCP21 and PROG1 . Quantitative RT‐PCR analysis of stem tissues at the jointing stage detected measurable expression for five of these genes. Four genes, OsTCP21 , OsFBL35 , OsFBA2 , and LOC_Os07g08190 , showed significant differential expression between tall and dwarf lines, whereas GID1L2 did not. The other three genes, including PROG1 , showed transcript levels too low for reliable detection. Haplotype analysis further identified coding and promoter variation in OsFBL35 , OsFBA2 , LOC_Os07g08190 , and GID1L2 , as well as promoter haplotypes in OsTCP21 . These results suggest that OsTCP21, OsFBL35 , OsFBA2 , LOC_Os07g08190 , and GID1L2 are potential candidate genes for plant height variation in this wild rice‐derived population. Functional annotation suggested that these candidates may be related to ubiquitination, hormone signaling, and growth regulation. These findings provide insight into the genetic basis of plant height variation derived from wild rice and offer candidate loci and molecular markers for rice improvement.

N6-methyladenosine (m⁶A) methylation functions as a vital post-transcriptional and epigenetic modification in higher plants regulated by α-ketoglutarate-dependent dioxygenases (ALKBH). However, the role of ALKBH genes in oriental melon (Cucumis melo L.) fruit ripening has not been explored. Therefore, we treated oriental melon with an exogenous m⁶A demethylase inhibitor (mechlorfenamic acid) then analyzed endogenous ethylene production and ripening-related indicators to explore the effects of m⁶A methylation on ripening. Bioinformatics and real-time quantitative PCR analyses were used to determine the impact of ALKBH genes on key ethylene synthesis gene expression. Treatment effectively inhibited endogenous ethylene production, firmness changes, and soluble solid contents, thereby extending fruit ripening. Eight ALKBH gene family members belonging to five major groups were identified in the melon genome. All members were expressed in ripening fruits, with different expression patterns during ripening. CmALKBH6, CmALKBH7, and CmALKBH8 expression was inhibited by an ethylene inhibitor (1-methylcyclopropene). The transient overexpression (OE) of CmALKBH8 in oriental melon led to the increased expression of the ethylene synthesis genes CmACS1, CmACS2, and CmACO1. In summary, the ethylene-regulated gene CmALKBH8 may participate in oriental melon fruit ripening regulation by modulating the methylation levels of ethylene synthesis-related genes. These findings help us better understand how m⁶A methylation regulates melon ripening.

Background: Rice has been used as a model plant to study adaptation, genome evolution and reproductive isolation among species and the genetics and evolution of complex traits. Two subspecies of cultivated rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. Results: To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica plants, and identified 97,005 transcribed fragments and 7702 novel transcriptionally active regions. We also identified 1857 (4.58% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. According to previous population genetic analyses, these DEGs may associate with the phenotypic differences between the two subspecies. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′ flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs.Conclusion: This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs that may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.