Erratum: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Zhou, Zhengkui; Jiang, Yu; Wang, Zheng; Gou, Zhiheng; Lyu, Jun; Li, Weiyu; Yu, Yong; Shu, Liping; Zhao, Yingjun; Ma, Yanming; Fang, Chao; Shen, Yanting; Liu, Tengfei; Li, Cong-Cong; Li, Qing; Wu, Mian; Wang, Min; Wu, Yunshuai; Dong, Yang; Wan, Wenting; Wang, Xiao; Ding, Zijing; Gao, Yue‐Dong; Xiang, Hui; Bao-cheng, Zhu; Lee, Suk-Ha; Wang, Wen; Tian, Zhixi

doi:10.1038/nbt0416-441c

Cited by 375 publications

(4 citation statements)

References 2 publications

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“…Notably, we also found that the θπ values of cultivated jute were lower than those of improved soybean (1.05 × 10 −3 ), the cultivated rice subspecies Indica ( Oryza sativa subsp. Indica; 1.6 × 10 −3 ), and improved sorghum (2.33 × 10 −3 ; Huang et al., 2012; Mace et al., 2013; Zhou et al., 2016). However, the F ST value between the cultivated lines and landraces was slightly higher for C. olitorius than for upland cotton (0.04; Fang et al., 2017; Ma et al., 2018) and pigeon pea (0.07; Varshney et al., 2017).…”

Section: Resultsmentioning

confidence: 99%

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Yang

Tian

et al. 2022

The Plant Journal

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SUMMARY Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi‐omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome‐wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole‐3‐acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

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Section: Resultsmentioning

confidence: 99%

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Yang

Tian

et al. 2022

The Plant Journal

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“…Identification of these genes is important for crop production. In the past few years, genome-wide association studies (GWAS) have been widely used in rice ( Huang et al, 2012 ), soybean ( Zhou et al, 2015 ), maize ( Tian et al, 2011 ), and melon ( Pereira et al, 2018 ) for the identification of important trait-controlled genes. It has also been used to identify flowering-related genes in Arabidopsis ( Aranzana et al, 2005 ), rice ( Liu et al, 2021 ), maize ( Maldonado et al, 2019 ), chrysanthemum ( Chong et al, 2019 ), and soybean ( Kim et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…The GWAS is powerful for identifying candidate genes corresponding to natural variation of traits in field crops as well as in horticultural plants ( Su et al, 2019 ; Alseekh et al, 2021 ; Berhe et al, 2021 ). A larger population size has been used for association analysis in field crops, such as rice ( Huang et al, 2012 ), soybean ( Zhou et al, 2015 ), and maize ( Maldonado et al, 2019 ). GWAS has also been identified in trait-related candidate genes or SNPs in horticultural plants using populations less than 100, such as rose ( Schulz et al, 2016 ), chestnut ( Kang et al, 2019 ), chrysanthemums ( Su et al, 2019 ), and bigleaf hydrangea ( Wu and Alexander, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies

Lü

et al. 2022

Front. Plant Sci.

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Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering phenotypes according to the time for floral induction. Early-flowering varieties need low chilling accumulation level for floral induction, whereas the late-flowering varieties require high chilling accumulation level. In the present study, RNA-Seq of 87 accessions was performed and transcriptome-based genome-wide association studies (GWAS) was used to identify candidate genes involved in chilling accumulation underlying the time for floral induction. A total of 98,155 high-quality single-nucleotide polymorphism (SNP) sites were obtained. A total of 1,411 significantly associated SNPs and 1,115 associated genes (AGs) were identified, of which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone signal transduction-related. Association analysis between the gene expression of the AGs and the flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate AGs (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal transduction-related CAGs were further screened. The expression levels of the CAGs in the early-flowering accessions were different from those in the late-flowering ones, and also between the flowering trees and non-flowering trees. In a gradient chilling treatment, flowering rates of the trees and the CAGs expression were affected by the treatment. Our present work for the first time provided candidate genes for genetic regulation of flowering in litchi using transcriptome-based GWAS.

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“…Over the next 10 years, researchers continuously performed resequencing and GWAS (Genome-Wide Association Studies) on wild and cultivated soybeans. The excavation of these genomic resources provides extremely important resources and platforms for soybean research, which will vigorously promote soybean molecular design and breeding, and help achieve the “green revolution” of soybeans [ 38 , 39 , 40 , 41 , 42 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

Development of an NLR-ID Toolkit and Identification of Novel Disease-Resistance Genes in Soybean

Shao,

Shi,

Chu

et al. 2024

Plants

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The recognition of pathogen effectors through the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. In addition to typical domains such as TIR, CC, NBS, and LRR, NLR proteins also contain some atypical integrated domains (IDs), the roles of which are rarely investigated. Here, we carefully screened the soybean (Glycine max) genome and identified the IDs that appeared in the soybean TNL-like proteins. Our results show that multiple IDs (36) are widely present in soybean TNL-like proteins. A total of 27 Gm-TNL-ID genes (soybean TNL-like gene encoding ID) were cloned and their antiviral activity towards the soybean mosaic virus (SMV)/tobacco mosaic virus (TMV) was verified. Two resistance (R) genes, SRA2 (SMV resistance gene contains AAA_22 domain) and SRZ4 (SMV resistance gene contains zf-RVT domain), were identified to possess broad-spectrum resistance characteristics towards six viruses including SMV, TMV, plum pox virus (PPV), cabbage leaf curl virus (CaLCuV), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV). The effects of Gm-TNL-IDX (the domain of the Gm-TNL-ID gene after the TN domain) on the antiviral activity of a R protein SRC7TN (we previously reported the TN domain of the soybean broad-spectrum resistance gene SRC7) were validated, and most of Gm-TNL-IDX inhibits antiviral activity mediated by SRC7TN, possibly through intramolecular interactions. Yeast-two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that seven Gm-TNL-IDX interacted with SMV-component proteins. Truncation analysis on a broad-spectrum antiviral protein SRZ4 indicated that SRZ4TIR is sufficient to mediate antiviral activity against SMV. Soybean cDNA library screening on SRZ4 identified 48 interacting proteins. In summary, our results indicate that the integration of IDs in soybean is widespread and frequent. The NLR-ID toolkit we provide is expected to be valuable for elucidating the functions of atypical NLR proteins in the plant immune system and lay the foundation for the development of engineering NLR for plant-disease control in the future.

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Erratum: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Cited by 375 publications

References 2 publications

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies

Development of an NLR-ID Toolkit and Identification of Novel Disease-Resistance Genes in Soybean

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