Plant genomics

    Default Latest Most Read
    Please wait a minute...
    For Selected: Toggle Thumbnails
      
    Genome-wide identification of loci affecting seed glucosinolate contents in Brassica napus L.
    Dayong Wei, Yixin Cui, Jiaqin Mei, Lunwen Qian, Kun Lu, Zhi-Min Wang, Jiana Li, Qinglin Tang and Wei Qian
    J Integr Plant Biol    2019, 61 (5): 611-623.   DOI: 10.1111/jipb.12717
    Accepted: 05 September 2018
    Online available: 05 September 2018

    Abstract331)            English Version    Save
    Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests. However, the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed (Brassica napus L.). To identify the loci affecting seed glucosinolate content (SGC), we conducted genome-wide resequencing in a population of 307 diverse B. napus accessions from the three B. napus ecotype groups, namely, spring, winter, and semi-winter. These resequencing data were used for a genome-wide association study (GWAS) to identify the loci affecting SGC. In the three ecotype groups, four common and four ecotype-specific haplotype blocks (HBs) were significantly associated with SGC. To identify candidate genes controlling SGC, transcriptome analysis was carried out in 36 accessions showing extreme SGC values. Analyses of haplotypes, genomic variation, and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs, respectively. Our expression analyses demonstrated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B. napus.
    Related Articles | Metrics
      
    Genomic divergence in cotton germplasm related to maturity and heterosis
    Shoupu He, Gaofei Sun, Longyu Huang, Daigang Yang, Panhong Dai, Dayun Zhou, Yuzhen Wu, Xiongfeng Ma, Xiongming Du, Shoujun Wei, Jun Peng and Meng Kuang
    J Integr Plant Biol    2019, 61 (8): 929-942.   DOI: 10.1111/jipb.12723
    Accepted: 25 September 2018
    Online available: 25 September 2018

    Abstract350)      PDF (22691KB)(177)       English Version    Save

    Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high‐quality single‐nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage‐specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity‐related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage‐specific regions and heterozygous loci, in the high‐yield hybrids, suggests a role for these regions in cotton heterosis.

    Related Articles | Metrics
      
    Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and flowering time in Brassica napus
    Fengqi Zhang, Junyan Huang, Minqiang Tang, Xiaohui Cheng, Yueying Liu, Chaobo Tong, Jingyin Yu, Tehrim Sadia, Caihua Dong, Lingyan Liu, Baojun Tang, Jianguo Chen and Shengyi Liu
    J Integr Plant Biol    2019, 61 (1): 75-88.   DOI: 10.1111/jipb.12754
    Accepted: 01 December 2018
    Online available: 01 December 2018

    Abstract279)            English Version    Save
    Oilseed rape (Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci (QTL) for stem rot resistance (SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time (FT) in a recombinant inbred line population. The population was genotyped using B. napus 60K single nucleotide polymorphism arrays and phenotyped in six (FT) and nine (SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co-localized, suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL-associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2-C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.
    Related Articles | Metrics
      
    Wheat and barley biology: Towards new frontiers
    Thorsten Schnurbusch
    J Integr Plant Biol    2019, 61 (3): 198-203.   DOI: 10.1111/jipb.12782
    Accepted: 29 January 2019
    Online available: 29 January 2019

    Abstract506)            Save
    Related Articles | Metrics
      
    An efficient TILLING platform for cultivated tobacco
    Yu-Long Gao, Xue-Feng Yao, Wen-Zheng Li, Zhong-Bang Song, Bing-Wu Wang, Yu-Ping Wu, Jun-Li Shi, Guan-Shan Liu, Yong-Ping Li and Chun-Ming Liu
    J Integr Plant Biol    2020, 62 (2): 165-180.   DOI: 10.1111/jipb.12784
    Accepted: 30 January 2019
    Online available: 30 January 2019

    Abstract1320)      PDF (736KB)(566)       English Version    Save

    Targeting‐induced local lesions in genomes (TILLING) is a powerful reverse‐genetics tool that enables high‐throughput screening of genomic variations in plants. Although TILLING has been developed for many diploid plants, the technology has been used in very few polyploid species due to their genomic complexity. Here, we established an efficient capillary electrophoresis‐based TILLING platform for allotetraploid cultivated tobacco (Nicotiana tabacum L.) using an ethyl methanesulfonate (EMS)‐mutagenized population of 1,536 individuals. We optimized the procedures for endonuclease preparation, leaf tissue sampling, DNA extraction, normalization, pooling, PCR amplification, heteroduplex formation, and capillary electrophoresis. In a test screen using seven target genes with eight PCR fragments, we obtained 118 mutants. The mutation density was estimated to be approximately one mutation per 106 kb on average. Phenotypic analyses showed that mutations in two heavy metal transporter genes, HMA2S and HMA4T, led to reduced accumulation of cadmium and zinc, which was confirmed independently using CRISPR/Cas9 to generate knockout mutants. Our results demonstrate that this powerful TILLING platform (available at http://www.croptilling.org) can be used in tobacco to facilitate functional genomics applications.

    Related Articles | Metrics
      
    Elicitor hydrophobin Hyd1 interacts with Ubiquilin1-like to induce maize systemic resistance
    Chuanjin Yu, Kai Dou, Shaoqing Wang, Qiong Wu, Mi Ni, Tailong Zhang, Zhixiang Lu, Jun Tang and Jie Chen
    J Integr Plant Biol    2020, 62 (4): 509-526.   DOI: 10.1111/jipb.12796
    Accepted: 25 February 2019
    Online available: 25 February 2019

    Abstract271)      PDF (54891KB)(157)       English Version    Save

    Trichoderma harzianum is a plant‐beneficial fungus that secretes small cysteine‐rich proteins that induce plant defense responses; however, the molecular mechanism involved in this induction is largely unknown. Here, we report that the class II hydrophobin ThHyd1 acts as an elicitor of induced systemic resistance (ISR) in plants. Immunogold labeling and immunofluorescence revealed ThHyd1 localized on maize (Zea mays) root cell plasma membranes. To identify host plant protein interactors of Hyd1, we screened a maize B73 root cDNA library. ThHyd1 interacted directly with ubiquilin 1‐like (UBL). Furthermore, the N‐terminal fragment of UBL was primarily responsible for binding with Hyd1 and the eight‐cysteine amino acid of Hyd1 participated in the protein‐protein interactions. Hyd1 from T. harzianum (Thhyd1) and ubl from maize were co‐expressed in Arabidopsis thaliana, they synergistically promoted plant resistance against Botrytis cinerea. RNA‐sequencing analysis of global gene expression in maize leaves 24 h after spraying with Curvularia lunata spore suspension showed that Thhyd1‐induced systemic resistance was primarily associated with brassinosteroid signaling, likely mediated through BAK1. Jasmonate/ethylene (JA/ET) signaling was also involved to some extent in this response. Our results suggest that the Hyd1‐UBL axis might play a key role in inducing systemic resistance as a result of Trichoderma‐plant interactions.

    Related Articles | Metrics
      
    Maize biology: From functional genomics to breeding application
    Jianbing Yan and Bao-Cai Tan
    J Integr Plant Biol    2019, 61 (6): 654-657.   DOI: 10.1111/jipb.12819
    Accepted: 17 May 2019
    Online available: 17 May 2019

    Abstract281)      PDF (154KB)(437)       Save
    Related Articles | Metrics
      
    The multi-omics basis of potato heterosis
    Dawei Li, Xiaoyue Lu, Yanhui Zhu, Jun Pan, Shaoqun Zhou, Xinyan Zhang, Guangtao Zhu, Yi Shang, Sanwen Huang and Chunzhi Zhang
    J Integr Plant Biol    2022, 64 (3): 671-687.   DOI: 10.1111/jipb.13211
    Accepted: 28 December 2021
    Online available: 28 December 2021

    Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.

    Related Articles | Metrics
    Cited: WebOfScience(15)
      
    Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)
    Yushan Zheng, Deming Yang, Jundong Rong, Liguang Chen, Qiang Zhu, Tianyou He, Lingyan Chen, Jing Ye, Lili Fan, Yubang Gao, Hangxiao Zhang and Lianfeng Gu
    J Integr Plant Biol    2022, 64 (3): 649-670.   DOI: 10.1111/jipb.13217
    Accepted: 06 January 2022
    Online available: 06 January 2022

    Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time long-read isoform sequencing revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
    Related Articles | Metrics
    Cited: WebOfScience(15)
      
    Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
    Bin‐Bin Liu, Chen Ren, Myounghai Kwak, Richard G.J. Hodel, Chao Xu, Jian He, Wen‐Bin Zhou, Chien‐Hsun Huang, Hong Ma, Guan‐Ze Qian, De‐Yuan Hong and Jun Wen
    J Integr Plant Biol    2022, 64 (5): 1020-1043.   DOI: 10.1111/jipb.13246
    Accepted: 11 March 2022
    Online available: 11 March 2022

    Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

    Related Articles | Metrics
    Cited: WebOfScience(22)
      
    The Larix kaempferi genome reveals new insights into wood properties
    Chao Sun, Yun‐Hui Xie, Zhen Li, Yan‐Jing Liu, Xiao‐Mei Sun, Jing‐Jing Li, Wei‐Peng Quan, Qing‐Yin Zeng, Yves Van de Peer and Shou‐Gong Zhang
    J Integr Plant Biol    2022, 64 (7): 1364-1373.   DOI: 10.1111/jipb.13265
    Accepted: 20 April 2022
    Online available: 20 April 2022

    Abstract374)            English Version    Save

    Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

    Related Articles | Metrics
    Cited: WebOfScience(12)
      
    Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition
    Shuo Zhang, Li Deng, Lun Zhao and Changyin Wu
    J Integr Plant Biol    2022, 64 (9): 1690-1705.   DOI: 10.1111/jipb.13325
    Accepted: 05 July 2022
    Online available: 05 July 2022

    Abstract333)            English Version    Save

    RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regulatory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to identify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome sequencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

    Related Articles | Metrics
      
    Recent progression and future perspectives in cotton genomic breeding
    Zhaoen Yang, Chenxu Gao, Yihao Zhang, Qingdi Yan, Wei Hu, Lan Yang, Zhi Wang and Fuguang Li
    J Integr Plant Biol    2023, 65 (2): 548-569.   DOI: 10.1111/jipb.13388
    Accepted: 13 October 2022
    Online available: 13 October 2022

    Abstract634)            English Version    Save
    Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate “super cotton”, synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
    Related Articles | Metrics
    Cited: WebOfScience(11)
      
    Phylogenomics and the flowering plant tree of life
    Cen Guo, Yang Luo, Lian-Ming Gao, Ting-Shuang Yi, Hong-Tao Li, Jun-Bo Yang and De-Zhu Li
    J Integr Plant Biol    2023, 65 (2): 299-323.   DOI: 10.1111/jipb.13415
    Accepted: 23 November 2022
    Online available: 23 November 2022

    Abstract341)            English Version    Save
    The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
    Related Articles | Metrics
    Cited: WebOfScience(14)
      
    Understandings and future challenges in soybean functional genomics and molecular breeding
    Haiping Du, Chao Fang, Yaru Li, Fanjiang Kong and Baohui Liu
    J Integr Plant Biol    2023, 65 (2): 468-495.   DOI: 10.1111/jipb.13433
    Accepted: 13 December 2022
    Online available: 13 December 2022

    Abstract204)            English Version    Save
    Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize–soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
    Related Articles | Metrics
    Cited: WebOfScience(9)
      
    Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
    Hongyin Hu, Pengchuan Sun, Yongzhi Yang, Jianxiang Ma and Jianquan Liu
    J Integr Plant Biol    2023, 65 (6): 1479-1489.   DOI: 10.1111/jipb.13455
    Accepted: 16 January 2023
    Online available: 16 January 2023

    Abstract214)            English Version    Save
    Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.
    Related Articles | Metrics
    Cited: WebOfScience(1)
      
    High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility
    Qiang He, Dan Ma, Wei Li, Longsheng Xing, Hongyu Zhang, Yu Wang, Cailian Du, Xuanzhao Li, Zheng Jia, Xiuxiu Li, Jianan Liu, Ze Liu, Yuqing Miao, Rui Feng, Yang Lv, Meijia Wang, Hongwei Lu, Xiaochen Li, Yao Xiao, Ruyu Wang, Hanfei Liang, Qinghong Zhou, Lijun Zhang, Chengzhi Liang and Huilong Du
    J Integr Plant Biol    2023, 65 (6): 1423-1441.   DOI: 10.1111/jipb.13459
    Accepted: 21 January 2023
    Online available: 21 January 2023

    Abstract274)            English Version    Save
    Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin- degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self- incompatibility in buckwheat.
    Related Articles | Metrics
    Cited: WebOfScience(5)
      
    Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated
    Chunlin Chen, Brad R. Ruhfel, Jialiang Li, Zefu Wang, Lushui Zhang, Lei Zhang, Xingxing Mao, Ji Wang, Dashan He, Yue Luo, Quanjun Hu, Yuanwen Duan, Xiaoting Xu, Zhenxiang Xi and Jianquan Liu
    J Integr Plant Biol    2023, 65 (6): 1490-1504.   DOI: 10.1111/jipb.13464
    Accepted: 07 February 2023
    Online available: 07 February 2023

    Abstract261)            English Version    Save
    Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.
    Related Articles | Metrics
    Cited: WebOfScience(2)
      
    Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites
    Irene Julca, Daniela Mutwil-Anderwald, Vaishnervi Manoj, Zahra Khan, Soak Kuan Lai, Lay K. Yang, Ing T. Beh, Jerzy Dziekan, Yoon P. Lim, Shen K. Lim, Yee W. Low, Yuen I. Lam, Seth Tjia, Yuguang Mu, Qiao W. Tan, Przemyslaw Nuc, Le M. Choo, Gillian Khew, Loo Shining, Antony Kam, James P. Tam, Zbynek Bozdech, Maximilian Schmidt, Bjoern Usadel, Yoganathan Kanagasundaram, Saleh Alseekh, Alisdair Fernie, Hoi Y. Li and Marek Mutwil
    J Integr Plant Biol    2023, 65 (6): 1442-1466.   DOI: 10.1111/jipb.13469
    Accepted: 21 February 2023
    Online available: 21 February 2023

    Abstract238)            English Version    Save
    Plants accumulate a vast array of secondary metabolites, which constitute a natural resource for pharmaceuticals. Oldenlandia corymbosa belongs to the Rubiaceae family, and has been used in traditional medicine to treat different diseases, including cancer. However, the active metabolites of the plant, their biosynthetic pathway and mode of action in cancer are unknown. To fill these gaps, we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression, metabolic profiles, and anti-cancer activity. Our results show that O. corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity. Moreover, we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid. Finally, we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking. Altogether, these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group, while the mode of action of ursolic acid will allow us to further develop this valuable compound.
    Related Articles | Metrics
    Cited: WebOfScience(2)
      
    Genomic convergence underlying high-altitude adaptation in alpine plants
    Xu Zhang, Tianhui Kuang, Wenlin Dong, Zhihao Qian, Huajie Zhang, Jacob B. Landis, Tao Feng, Lijuan Li, Yanxia Sun, Jinling Huang, Tao Deng, Hengchang Wang and Hang Sun
    J Integr Plant Biol    2023, 65 (7): 1620-1635.   DOI: 10.1111/jipb.13485
    Accepted: 24 March 2023
    Online available: 24 March 2023

    Abstract215)            English Version    Save
    Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.
    Related Articles | Metrics
      
    An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence
    Jun‐Tong Chen, Magnus Lidén, Xian‐Han Huang, Liang Zhang, Xin‐Jian Zhang, Tian‐Hui Kuang, Jacob B. Landis, Dong Wang, Tao Deng and Hang Sun
    J Integr Plant Biol    2023, 65 (9): 2138-2156.   DOI: 10.1111/jipb.13499
    Accepted: 29 April 2023
    Online available: 29 April 2023

    Abstract197)            English Version    Save
    The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent “series”. Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five “series”, 25 sections and one “series” are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.
    Related Articles | Metrics
    Cited: WebOfScience(2)
      
    Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome
    Yarong Lin, Yiwang Zhu, Yuchao Cui, Hongge Qian, Qiaoling Yuan, Rui Chen, Yan Lin, Jianmin Chen, Xishi Zhou, Chuanlin Shi, Huiying He, Taijiao Hu, Chenbo Gu, Xiaoman Yu, Xiying Zhu, Yuexing Wang, Qian Qian, Cuijun Zhang, Feng Wang and Lianguang Shang
    J Integr Plant Biol    2023, 65 (12): 2541-2551.   DOI: 10.1111/jipb.13568
    Accepted: 20 September 2023
    Online available: 20 September 2023

    Abstract222)            English Version    Save
    Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for the development of high-yield and thermotolerant rice varieties.
    Related Articles | Metrics
      
    10k-level integrated rice database shows power for exploiting rare variants
    Hong Yu, Liquan Kou and Jiayang Li
    J Integr Plant Biol    2023, 65 (12): 2539-2540.   DOI: 10.1111/jipb.13576
    Accepted: 25 October 2023
    Online available: 25 October 2023

    Abstract126)            English Version    Save
    Related Articles | Metrics