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Global climate change poses a severe threat to mountain biodiversity. Phenotypic plasticity and local adaptation are two common strategies for alpine plant to cope with such change. They may facilitate organismal adaptation to contrasting environments, depending on the influences of the environment or genotype or their interacted effects. In this study, we use an endemic alpine plant (Rorippa elata) in the Hengduan mountains (HDM) to unravel its phenotypic basis of adaptation strategy and evaluate the relative contributions of environment and genotype to its phenotype. We transplanted 37 genotypes of R. elata into two common gardens across low and high elevations (2800 vs. 3800 m) during 2021–2022. Nine fitness-related traits were measured, including flowering probability and glucosinolates (GS) content. We estimated the environmental or genotypic contributions to the phenotype and identified the main environmental components. Our results revealed that both environment and genotype-by-environment interactions contributed to the phenotypes of R. elata. Latitudinal heterogeneity was identified as a key factor that explained 24% of the total phenotypic variation. In particular, genotypes of the northern HDM showed significantly higher plasticity in flowering probability than those of the southern HDM. Furthermore, within the southern HDM, GS content indicated local adaptation to herbivory stresses for R. elata genotypes along elevations. In conclusion, our results suggest that R. elata may have adapted to the alpine environment through species-level plasticity or regional-level local adaptation. These processes were shaped by either complex topography or interactions between genotype and mountain environments. Our study provides empirical evidence on the adaptation of alpine plants. [ABSTRACT FROM AUTHOR]

As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber‐type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio‐temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next‐generation sequencing technology, the integration of quantitative trait loci mapping with genome‐wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in‐depth understanding and utilization remain, and the cost of large‐scale sequencing, which requires integrated analyses of high‐throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs. [ABSTRACT FROM AUTHOR]

Alternative polyadenylation (APA) generates different 3′‐untranslated regions (3′UTRs) to regulate gene expression and localization, and affects a variety of biological processes. Here, we characterized the 3′UTR dynamics during the oocyte‐to‐zygote transition by analysing our previously reported porcine single‐cell RNA‐seq (scRNA‐seq) datasets (in vitro matured metaphase II (MII) oocytes, in vitro fertilized zygotes (IVF1) and parthenogenetically activated 1‐cell embryos (PA1)). After IVF1 versus MII comparison, dynamic analyses of APA from RNA‐seq (DaPars) method identified 139 mRNAs with significantly different 3′UTRs (padj. ≤.05), mainly enriched in cell cycle, regulation of cyclin‐dependent protein kinase activity, histone modification, mRNA surveillance, and regulation of actin cytoskeleton. For PA1 versus MII comparison, 105 mRNAs with significantly different 3′UTRs (padj. ≤.05) were identified to be mainly enriched in intracellular transport, mitotic spindle organization, cell cycle, pyruvate metabolism and glycolysis/gluconeogenesis. Furthermore, there were 7 mRNAs with more significant 3′UTR differences (|△PDUI| ≥ 0.45 and |log2[PDUI ratio]| ≥ 0.59) respectively in IVF1 versus MII (Lrp2bp, Mtfr2, Nhlrc2, Psip1, Smu1, Ssr1 and Wtap) and PA1 versus MII (Asf1b, Dimt1, Nap1l1, Ncoa4, Nudt21, Pnn and Rpl15) comparisons. Integrative genomics viewer analysis further identified that 3′UTRs of Psip1, Smu1, Ssr1 and Wtap had more than 140 nt average length changes, whereas those of Dimt1, Nap1l1 and Rpl15 were shortened with more than 460 nt. Regulatory elements (PAS, CPE, microRNA binding sites and m6A sites) in 3′UTRs of different lengths were predicted. Our findings provide useful information to further investigate the molecular mechanism of 3′UTR in regulating the oocyte‐to‐zygote transition of pig embryos. [ABSTRACT FROM AUTHOR]