The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

The origin and evolution of carpels and fruits from an evo-devo perspective

The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and stamens.Therefore,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology.Here,we briefly summarize the main progress and key genes identified for understanding floral development,focusing on the origin and development of the carpels.Floral ABC models have played pioneering roles in elucidating flower development,but remain insufficient for resolving flower and carpel origin.The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive.Based on current research progress and technological advances,simplified floral models and integrative evolutionary-developmental(evodevo)strategies are proposed for elucidating the genetics of carpel origin and fruit evolution.Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes.Among the identified transcription factors,AGAMOUS(AG)and CRABS CLAW(CRC)may be the two core regulatory genes for carpel origin as they determine carpel organ identity,determinacy,and functionality.Therefore,a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.

Isolation and characterization of soybean NBS analogs

Isolation of plant resistance genes is greatly helpful to crop resistance breeding and the insight of resistance mechanism. The cloned plant resistance genes are classified into four classes according to their putative structural domain, of which the majority possesses nucleotide-binding site (NBS) domain that consists of P-loop, kinase2a and kinase3a. The conservation of this domain affords the potential possibility of cloning the plant resistance genes, which is homology-based cloning technique. In the present study, the degenerate oligonucleotide primers were designed according to the tobacco N and Arabidopsis RPS2, and 358 clones were isolated from the genomic DNA of resistance soybean culti-var Kefengl, resistant to soybean mosaic virus, and 4 open-reading NBS analogs were finally characterized and designated as KNBS1, KNBS2, KNBS3 and KNBS4. Southern hybridization suggested that they were present with multicopy in the soybean genome; KNBS4 was mapped to F linkage group and KNBS2 co-located J

A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication

The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development.Here,we present such a rare and potential case of“to gain by loss”as a neomorphic mutation during soybean domestication for increasing seed weight.Using a population derived from a chromosome segment substitution line of Glycine max(SN14)and Glycine soja(ZYD06),a quantitative trait locus(QTL)of 100-seed weight(q HSW)was mapped on chromosome 11,corresponding to a truncatedβ-1,3-glucosidase(βGlu)gene.The novel gene hsw results from a 14-bp deletion,causing a frameshift mutation and a premature stop codon in theβGlu.In contrast to HSW,the hsw completely lostβGlu activity and function but acquired a novel function to promote cell expansion,thus increasing seed weight.Overexpressing hsw instead of HSW produced large soybean seeds,and surprisingly,truncating hsw via gene editing further increased the seed size.We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size.Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control.Moreover,the hsw allele underwent selection and expansion during soybean domestication and improvement.Our work cloned a likely domesticated QTL controlling soybean seed weight,revealed a novel genetic variation and mechanism in soybean domestication,and provided new insight into crop domestication and breeding,and plant evolution.

Current development and application of soybean genomics

Soybean (Glycine max), an important domesticated species originated in China, constitutes a major source ofedible oils and high-quality plant proteins worldwide. In spite of its complex genome as a consequence of an ancienttetraploidilization, platforms for map-based genomics, sequence-based genomics, comparative genomics and functionalgenomics have been well developed in the last decade, thus rich repertoires of genomic tools and resources are available,which have been influencing the soybean genetic improvement. Here we mainly review the progresses of soybean(including its wild relative Glycine soja) genomics and its impetus for soybean breeding, and raise the major biologicalquestions needing to be addressed. Genetic maps, physical maps, QTL and EST mapping have been so well achievedthat the marker assisted selection and positional cloning in soybean is feasible and even routine. Whole genomesequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes, which areinstrumental to comparative genomics and functional genomics. Comparative genomics has started to reveal theevolution of soybean genome and the molecular basis of soybean domestication process. Microarrays resources,mutagenesis and efficient transformation systems become essential components of soybean functional genomics.Furthermore, phenotypic functional genomics via both forward and reverse genetic approaches has inferred functionsof many genes involved in plant and seed development, in response to abiotic stresses, functioning in plant-pathogenicmicrobe interactions, and controlling the oil and protein content of seed. These achievements have paved the way forgeneration of transgenic or genetically modified (GM) soybean crops.