SUMMARY Root system architecture (RSA) varies across environments and plays essential roles in plant adaptive growth. Auxin and its polar transport have been found to be key players in the regulation of RSA. However, the molecular mechanisms underlying the regulation of RSA in fluctuating environments remain unclear. Using a forward genetic screen for root mutants under gravitropism interference conditions in the model plant Arabidopsis thaliana , we revealed that HYPERSENSITIVE TO IBUPROFEN1 ( HIB1 ) regulates root gravitropic growth and RSA by modulating auxin distribution in Arabidopsis. The hib1 seedlings presented defects in primary root elongation, lateral root organogenesis, and the root gravitropic response because of abnormal auxin distribution. Notably, the gravitropic defects of hib1 roots were correlated with increased MPK6 activity and could be rescued by loss‐of‐function mpk6 mutation. Furthermore, cell biological results revealed that HIB1 regulated PIN protein polar distribution and abundance at the plasma membrane, indicating that HIB1 is involved in polar auxin transport and the subsequent auxin response. Indeed, genetic perturbation of HIB1 results in impaired gravitropic root growth. Our work revealed that the HIB1‐auxin module regulates root gravitropism and RSA, providing insights into the molecular mechanisms underlying adaptive root growth.
SUMMARY Speciation is the fundamental process driving the origin of earth biodiversity. While speciation mechanisms have been revealed in many plant taxa, the evolutionary dynamics of heterosporous lycophytes remain largely unexplored. Here, we used the Selaginella sanguinolenta group, comprising seven montane species in eastern Asia, as a model system. We generated a high‐quality, chromosome‐level reference genome for S . aitchisonii , conducted whole‐genome resequencing of 191 individuals across 49 populations, and integrated population genomic, phylogenomic, morphological, and ecological analyses. Our results revealed that strong geographic isolation, driven by Miocene paleogeographic events, led to high genetic differentiation and restricted interspecific gene flow. The unique combination of heterospory and independent gametophyte generations might exacerbate extreme inbreeding, further impeding the ability of these lineages to surmount geographical barriers. Ecological niche divergence indicated that these species experience heterogeneous selection pressures; moreover, evidence of selective sweeps, leaf arrangement variation, and functional gene divergence indicates that natural selection gives rise to new species with environmentally adaptive traits. Demographic reconstructions revealed a shared trajectory of expansion followed by contraction into bottlenecks from the late Miocene to the Pliocene. Montane refugia likely played a role in species persistence, preserving genetic diversity for the postglacial expansions observed in four species since the Last Interglacial. We conclude that the S. sanguinolenta group underwent allopatric speciation since the Miocene and successfully persisted through severe Quaternary climatic fluctuations, which provides novel insights based on population genomic analysis into the evolution of early‐diverging vascular plants.
SUMMARY Bud sport is a common and stable somatic variation in perennial fruit trees. Loquat ( Eriobotrya japonica L.) is an evergreen fruit tree that can be categorized into yellow‐fleshed and white‐fleshed types based on the flesh color. To uncover the genetic basis, we herein assembled two nearly complete genomes for a yellow‐fleshed ‘Dongting’ loquat (TBY) and its white‐fleshed bud sport (TBW). The final sizes of assemblies were 773.29 Mb and 728.86 Mb with contig N50 of 31.87 Mb and 28.63 Mb for TBY and TBW, respectively. Comparative genomics analysis indicated that the heterozygosity ratio of TBY was nearly two‐fold higher than that of TBW (0.53% vs. 0.27%). Integrated multi‐omics and molecular marker detection results revealed that homozygosity of the EjPSY2A d / EjPSY2A d allele is the cause of the change in flesh color from yellow to white in TBY. Additionally, EjSUSs ( −1 , −2 , −3 , −12 ) and EjSPS3 might be the key genes responsible for the significant accumulation of hexoses and sucrose, respectively, in the flesh of TBY and TBW. Furthermore, high expression of EjC4H8 and Ej4CLs ( −7 , −10 , −20 ) in TBY might lead to the accumulation of more lignin in its flesh. Taken together, these findings provide valuable insights into the molecular mechanism differences between yellow‐ and white‐fleshed loquat and highlight the significance of bud sport as a valuable approach for generating novel germplasm resources in fruit trees.
SUMMARY The universal iron–sulfur (Fe‐S) clusters embedded in proteins support numerous fundamental biological processes. However, many proteins involved in Fe‐S assembly machineries remain poorly characterized in plants. Here, we revealed that BOLA1 and BOLA4, two members of the BOLA family previously described as Fe‐S assembly factors in various organisms, are critical growth regulators that play a role in Fe homeostasis in Arabidopsis thaliana . Expression analyses showed that BOLA1 and BOLA4 are ubiquitously expressed across most Arabidopsis tissues. Using protoplast transfection assays, we also demonstrated that both BOLA‐GFP fusion proteins localize to chloroplasts and mitochondria. Mutant analyses revealed that while single bola1 or bola4 knock‐out mutants are phenotypically indistinguishable from the wild type, double bola1 bola4 mutants display severe growth defects, including early growth arrest of the primary root. Notably, this phenotype was rescued by grafting a wild‐type root system onto the bola1 bola4 aerial part. Fe quantification, Perls staining, and RT‐qPCR analyses further demonstrated that bola1 bola4 double mutants exhibit altered Fe distribution and Fe‐homeostasis‐related gene expression. Overall, our findings show that BOLA1 and BOLA4 act redundantly to maintain primary root growth and rosette development and are essential players in Fe signaling and partitioning in Arabidopsis.
SUMMARY Precise regulation of flowering time and maturity is critical for achieving high and stable soybean yields, and the circadian clock plays a central role in coordinating these developmental transitions. Soybean is a typical short‐day crop with a pronounced photoperiodic response; however, the molecular mechanisms linking circadian regulation to photoperiod‐dependent flowering and maturity remain incompletely understood. Here, we integrated genome‐wide association analysis with deep learning approaches using 257 soybean germplasm accessions spanning 14 maturity groups and identified GmRVE8a , a homolog of the Arabidopsis circadian clock gene REVEILLE , as a strong candidate locus associated with soybean maturity across two field environments. Haplotype analysis demonstrated that accessions carrying the GmRVE8a H1 haplotype consistently flowered and matured significantly later than those carrying GmRVE8a H2 . Functional validation revealed that knockout of GmRVE8a markedly accelerated flowering and maturity, whereas overexpression of GmRVE8a significantly delayed both processes. qRT‐PCR assays further suggested that GmRVE8a may repress flowering and delay maturity by promoting the expression of GmFT4 , a flowering‐inhibitory member of the FT family, and is unlikely to act by directly regulating E1 expression. Collectively, our findings suggest GmRVE8a as a circadian clock‐associated negative regulator of soybean flowering and maturity, and highlight it as a promising candidate for molecular breeding aimed at improving adaptation to diverse photoperiodic environments.
