Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube

Li, Hongtai; Gao, Wei; Xue, Chaoling; Zhang, Yao; Liu, Zhiguo; Zhang, Yu; Meng, Xu; Liu, Mengjun; Zhao, Jin

doi:10.1186/s12864-019-5936-2

Cited by 38 publications

(48 citation statements)

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“…Recently, more and more researches reveal that bHLH gene play important role in fruit development process, including tomato [11], peach [19], apple [20], almond [33] and Chinese jujube [34]. In this study, 91 HrbHLH mRNAs had an RPKM value greater than 1 in three fruit development stages.…”

Section: Discussionmentioning

confidence: 62%

“…Furthermore, four bHLH genes showed preferential tissue-speci c expression, including one gene (HrbHLH35) in leaf, two genes (HrbHLH43 and HrbHLH58) in fruit, one gene (HrbHLH63) in stem. The speci c accumulation of these bHLH genes in a particular tissue suggests that they may play conserved regulatory roles in discrete cells, organs, or conditions [20,34].…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

et al. 2020

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Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

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Section: Discussionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

et al. 2020

Preprint

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“…Despite the large number of available germplasm accessions, jujube has a few improved cultivars in comparison to other major fruit trees. So far most of the cultivars used in production are landraces and traditional cultivars historically selected by farmers [6,52]. As summarized above, jujube breeding is still in a primitive stage and host resistance against various species and isolates of pathogens have not been clearly identified, especially in the cases of JFSD and JFRD.…”

Section: Knowledge Gaps and Research Needs In Breeding Methodsmentioning

confidence: 99%

“…There are more than 900 jujube cultivars in China, which vary widely in traits such as leaf shape, fruit form, size, color, flavor, keeping quality and fruiting season [6]. These cultivars have been traditionally classified based on morphological characteristics [5,52]. Jujube has a long history of being introduced and exchanged among different regions in China and different countries and continents.…”

Section: Cultivar Mislabelingmentioning

confidence: 99%

Genetic Improvement of Chinese Jujube for Disease Resistances: Status, Knowledge Gaps and Research Needs

2019

Crop Breed Genet Genom.

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Chinese jujube is one of the earliest domesticated fruit trees in the world. This fruit crop is becoming increasingly popular globally for its outstanding adaptability to marginal land and a broad range of climate conditions. There is a growing demand by growers and consumers for new cultivars with improved yields, earliness, resistance to biotic and abiotic stresses and fruit quality attributes. Breeding jujube for disease resistance is still in its infancy despite the consensus that disease is the top-ranking production constraint and growing disease resistant cultivars is the most sustainable and cost-effective approach for diseases management. Major knowledge gaps remain to be filled in the current breeding scheme for enhancing disease resistance. These knowledge gaps include, but are not limited to (1) a lack of understanding of jujube pathogens in terms of their taxonomy, epidemiology and genetic diversity; (2) a lack of standardized screening methods to identify host resistance; (3) a high rate of germplasm mislabeling; and (4) ineffective production of hybrid progenies. Nonetheless, recent progress in utilization of male sterile parents in controlled crosses, coupled with mounting genomic information on both pathogens and jujube, will likely speed up the combination of host resistance with other horticultural traits. This article reviews the status of jujube disease resistance breeding and suggests future research needs for developing disease resistant cultivars of Chinese jujube. Although the review focuses on jujube breeding programs in China, the summarized information should be useful to researchers in the international jujube community as well.

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“…Specific reference genes for RT-qPCR of jujube were selected under a variety of conditions and sourced from different tissues/organs, fruit development stages, and biotic/abiotic stresses, providing more choices for further gene expression analysis and functional studies in jujube [22][23][24][25][26] .…”

Section: De Novo Genome Sequencing and Pseudochromosome Constructionmentioning

confidence: 99%

The historical and current research progress on jujube–a superfruit for the future

et al. 2020

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Jujube (Ziziphus jujuba Mill.), or Chinese date, is the most important species of Rhamnaceae, a large cosmopolitan family, and is one of the oldest cultivated fruit trees in the world. It originates from the middle and lower reaches of the Yellow River, the 'mother river' of the Chinese people. It is distributed in at least 48 countries on all continents except Antarctica and is becoming increasingly important, especially in arid and semiarid marginal lands. Based on a systematic analysis of the unique characteristics of jujube, we suggest that it deserves to be recognized as a superfruit. We summarized historical research achievements from the past 3000 years and reviewed recent research advances since 1949 in seven fields, including genome sequencing and application, germplasm resources and systematic taxonomy, breeding and genetics, cultivation theory and techniques, pest control, postharvest physiology and techniques, and nutrition and processing. Based on the challenges facing the jujube industry, we discuss eight research aspects to be focused on in the future.

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Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube

Cited by 38 publications

References 48 publications

Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

Genetic Improvement of Chinese Jujube for Disease Resistances: Status, Knowledge Gaps and Research Needs

The historical and current research progress on jujube–a superfruit for the future

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