Plant genomics

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    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
    Abstract (Browse 248)  |   Save
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    Wheat and barley biology: Towards new frontiers
    Thorsten Schnurbusch
    J Integr Plant Biol 2019, 61 (3): 198-203.  
    doi: 10.1111/jipb.12782
    Abstract (Browse 482)  |   Save
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    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
    Abstract (Browse 247)  |   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.

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    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
    Abstract (Browse 1283)  |   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.

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    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
    Abstract (Browse 307)  |   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.
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    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
    Abstract (Browse 249)  |   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.
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    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
    Abstract (Browse 320)  |   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.

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