Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress

Shu, Yongjun; Li, Wei; Zhao, Jianfeng; Zhang, Sijia; Xu, Hanyun; Liu, Ying; Guo, Changhong

doi:10.1590/1678-4685-gmb-2017-0053

Cited by 30 publications

(30 citation statements)

References 38 publications

(46 reference statements)

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“…Expression analysis of CBF related genes from M. trunctatula in alfalfa indicated that the genes (MsCBFl-17 and MsCBFl-18) are potential functional homologs of CBF3 [33]. The CBF homologs and gene group were located not only on M. trucatula chromosome 6, but also on chromosome 5 [33,34] on which we also detected several QTL associated with freezing sensitivity and a favorable QTL (BR-d2) ( Table 2). Therefore, the genomic regions of chromosome 6 and 5 where we detected QTL are crucial for alfalfa freezing tolerance improvement.…”

Section: Ft Qtl and Potential Applicationmentioning

confidence: 68%

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

Adhikari¹,

Makaju²,

Lindstrom³

et al. 2020

Preprint

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Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were phenotyped for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping by sequencing (GBS) and the QTL associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps; clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is useful as an indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL for four traits; visual rating-based FT, percentage survival (PS), treated to control regrowth ratio (RR), and treated to control biomass ratio (BR). Some QTL overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) potentially represented the genic region of a cold tolerance gene, the c-repeat binding factor (CBF). These QTL were located on the terminal end of chromosome 6 which is considered a location of the CBF homologs in alfalfa.Conclusions The indoor freezing tolerance selection method reported here is valuable for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources needed by the alfalfa research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

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Section: Ft Qtl and Potential Applicationmentioning

confidence: 68%

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

Adhikari¹,

Makaju²,

Lindstrom³

et al. 2020

Preprint

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“…As a signal molecule, hormones plays an important role in regulating gene expression which confirmed the results of the study on Medicago sativa (cv. Zhaodong) under cold and freezing stress response [16]. Therefore, this study was indicated that changing in the balance of alfalfa hormones in the field under low 11 temperature might affect the winter hardiness of alfalfa.…”

Section: Hormones In Alfalfa Response To Low Temperature Stressmentioning

confidence: 82%

“…At present, the most widely studied C-repeat-binding factor (CBF) signaling pathway including CBF1, CBF2, CBF3, and CBF transcription factor regulates the expression of COLD-RESPONSIVE (COR) functional gene, which is a component of the low-temperature signal transduction pathway, thereby improving the cold tolerance of plants [12,13]. So far, a number of studies have shown that CBF signaling pathway can improve the low temperature tolerance of various plants such as Arabidopsis thaliana [14,15], Medicago sativa [16], Triticum aestivum [17], Glycine max [18], and Malus domestica [19]. Overexpression of cloned MtCBF3 from Medicago truncatula induces COR gene expression and enhances low temperature tolerance of transgenic plants [20].…”

Section: Introductionmentioning

confidence: 99%

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

Wang

Jin

Meng

et al. 2019

Preprint

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Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown of alfalfa is an important storage organ in the process of wintering, and it is closely related to the winter hardiness of alfalfa. At present, the specific molecular mechanism of response to winter hardiness in alfalfa root crown is unclear. The transcriptome database created by RNA sequencing (RNA-seq) is widely used to identify the critical genes related to winter hardiness. Results: The transcriptomes of alfalfa varieties, such as “Lomgmu 806” (with high winter survival rate) and “Sardi” (with low winter survival rate) have been sequenced in the study. Among the identified 57,712 unigenes, 2,299 differentially expressed genes (DEGs) were up-regulated, and 2,143 unigenes were down-regulated in the Lomgmu 806 vs Sardi root crown. The KEGG pathway annotations showed that 1,159 unigenes were mainly annotated to 116 pathways. Seven DEGs belonging to “plant hormone signaling transduction”, “peroxidase” pathway and transcription factors family (MYB, B3, AP2/ERF, WRKY) genes involved in alfalfa winter hardiness. Among them, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliable results of transcriptome sequencing analyses. Conclusions: RNA-Seq was used to discover genes associated with the wintering differences between alfalfa varieties. The transcriptome data showed that the gene regulation response of alfalfa to low temperature stress, which provides a valuable resource for further identification and functional analysis of candidate genes for winter hardiness of alfalfa. In addition, these data provide references for future study of genetic breeding and winter hardiness in alfalfa.

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“…Hormones, as signalling molecules, play very important roles in regulating CBF gene expression in response to cold and freezing stresses in M. sativa (cv. Zhaodong) [18]. In summary, it is likely that Longmu 806 alfalfa has stronger winter hardiness than Sardi alfalfa due to the high levels of accumulated plant hormones.…”

Section: Discussionmentioning

confidence: 98%

“…sativa [17,18]. This suggests that the regulation of the CBF pathway may have a potential role in improving the low-temperature tolerance of alfalfa, although it may not be the only method by which low-temperature tolerance is improved.…”

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confidence: 99%

Differential expression analysis of genes in the root crown of alfalfa under low-temperature stress

Wang

Jin²,

Meng

et al. 2019

Preprint

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Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown is an important storage organ of alfalfa, especially in the wintering process, as it is closely related to winter hardiness. However, the molecular mechanism underlying the winter hardiness of the alfalfa root crown remains unclear. To investigate these gaps in knowledge, the RNA sequencing (RNA-Seq) technology was used to identify critical genes related to winter hardiness. Results: In this study, the winter survival rate of the Lomgmu 806 variety was approximately 3.68-fold higher than that of the Sardi variety. We sequenced the transcriptomes of the root crown of the two alfalfa varieties. Among the 57,712 unigenes identified, 2,299 differentially expressed genes (DEGs) were upregulated, and 2,143 DEGs were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations showed that 1,159 unigenes were mainly annotated in 116 pathways. Seven DEGs belonging to the “plant hormone signalling transduction” pathway, the “peroxisome” pathway and transcription factor family (MYB, B3, AP2/ERF, and WRKY) and involved in alfalfa winter hardiness were identified. As a result, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliability of the RNA-Seq analyses. Conclusions: The RNA-Seq data revealed the gene regulation response of alfalfa to low-temperature stress, which provides a valuable resource for the further identification and functional analysis of candidate genes related to winter hardiness in alfalfa. Furthermore, these data provide references for future in-depth studies of winter hardiness mechanisms in alfalfa.

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Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress

Cited by 30 publications

References 38 publications

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

Differential expression analysis of genes in the root crown of alfalfa under low-temperature stress

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