Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits

Long, Ruicai; Zhang, Fan; Zhang, Zhiwu; Li, Mingna; Chen, Lin; Wang, Xue; Liu, Wenwen; Zhang, Tiejun; Yu, Long‐Xi; He, Fei; Jiang, Xueqian; Yang, Xijiang; Yang, Ching Hong; Wang, Zhen; Yang, Qingchuan

doi:10.1016/j.gpb.2022.01.002

Cited by 33 publications

(36 citation statements)

References 79 publications

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“…A noteworthy characteristic of alfalfa is its plasticity in terms of its adaptation to complicated and changeable environmental and climatic conditions [28]. The release of chromosome-level genome assembly with 32 chromosomes of alfalfa cultivar Zhongmu-4 has provided abundant data resources for selecting drought-related genes and improving alfalfa drought resistance [29]. However, a comprehensive insight into the participation of the UGT family in adaptation of alfalfa to drought environments is lacking.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress

Han

Wang

et al. 2022

IJMS

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Drought stress is one of the major constraints that decreases global crop productivity. Alfalfa, planted mainly in arid and semi-arid areas, is of crucial importance in sustaining the agricultural system. The family 1 UDP-glycosyltransferases (UGT) is indispensable because it takes part in the regulation of plant growth and stress resistance. However, a comprehensive insight into the participation of the UGT family in adaptation of alfalfa to drought environments is lacking. In the present study, a genome-wide analysis and profiling of the UGT in alfalfa were carried out. A total of 409 UGT genes in alfalfa (MsUGT) were identified and they are clustered into 13 groups. The expression pattern of MsUGT genes were analyzed by RNA-seq data in six tissues and under different stresses. The quantitative real-time PCR verification genes suggested the distinct role of the MsUGT genes under different drought stresses and abscisic acid (ABA) treatment. Furthermore, the function of MsUGT003 and MsUGT024, which were upregulated under drought stress and ABA treatment, were characterized by heterologous expression in yeast. Taken together, this study comprehensively analyzed the UGT gene family in alfalfa for the first time and provided useful information for improving drought tolerance and in molecular breeding of alfalfa.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress

Han

Wang

et al. 2022

IJMS

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“…Its first applications to alfalfa biomass yield profited from the development of high‐throughput genotyping techniques, such as genotyping‐by‐sequencing (GBS) (Elshire et al., 2011), which can generate thousands of single‐nucleotide polymorphism (SNP) data for a low cost in alfalfa (Li, Wei, et al., 2014) and other crops. Adopting Ape kI as the restriction enzyme according to Elshire et al.’s (2011) protocol would be supported by the fact that ∼56% of the alfalfa genome includes repetitive DNA sequences (Long et al., 2022), which this enzyme tends to skip. The potential of GS for alfalfa biomass yield has been investigated based on phenotyping data collected in specific cropping environments.…”

Section: Introductionmentioning

confidence: 99%

Alfalfa genomic selection for different stress‐prone growing regions

Annicchiarico

Bouizgaren

et al. 2022

The Plant Genome

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Alfalfa (Medicago sativa L.) selection for stress-prone regions has high priority for sustainable crop-livestock systems. This study assessed the genomic selection (GS) ability to predict alfalfa breeding values for drought-prone agricultural sites of Algeria, Morocco, and Argentina; managed-stress (MS) environments of Italy featuring moderate or intense drought; and one Tunisian site irrigated with moderately saline water. Additional aims were to investigate genotype × environment interaction (GEI) patterns and the effect on GS predictions of three single-nucleotide polymorphism (SNP) calling procedures, 12 statistical models that exclude or incorporate GEI, and allele dosage information. Our study included 127 genotypes from a Mediterranean reference population originated from three geographically contrasting populations, genotyped via genotyping-by-sequencing and phenotyped based on multi-year biomass dry matter yield of their dense-planted half-sib progenies. The GEI was very large, as shown by 27-fold greater additive genetic variance × environment interaction relative to the additive genetic variance and low genetic correlation for progeny yield responses across environments. The predictive ability of GS (using

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“…However, few studies have researched UGT genes in alfalfa, and the biological role of UGTs associated with secondary metabolism has not been understood until now. Recently, the genome sequence data of the autotetraploid plant alfalfa has been gradually completed ( Chen H. et al, 2020 ; Shen et al, 2020 ; Long et al, 2022 ), providing valuable genomic information and making it possible to identify and research the function of the UGT gene family in alfalfa at the genome-wide level. In this study, we performed a systematic genome-wide analysis to identify UGT family genes in alfalfa and screened 90 of them for their association with secondary metabolism.…”

Section: Introductionmentioning

confidence: 99%

“…

Long R and Li M (2022) Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa (Medicago sativa L.).

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mentioning

confidence: 99%

Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa (Medicago sativa L.)

Jiang²,

Sun³

et al. 2022

Front. Plant Sci.

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Uridine diphosphate glycosyltransferases (UGTs) are enzymes that catalyze glycosylation modifications and play an essential role in regulating plant metabolism. Alfalfa (Medicago sativa L.) is the most important legume in the world due to its high yields and protein content; however, the UGT genes in alfalfa have not yet been studied. Identifying UGT genes with metabolic roles in alfalfa is essential for identifying and modifying genetic traits that are relevant to yield and quality. In this study, 90 of the 239 UGT genes identified from the alfalfa “Zhongmu No. 1” genome database were found to be related to secondary metabolism, and a series of gene family characterization analyses were conducted on each. The results demonstrated that all 90 UGT genes were unevenly distributed on eight chromosomes with few introns and that tandem duplications were the crucial driving force expanding the UGT family in alfalfa. Notably, the 90 UGT genes can be clustered into ten evolutionary groups which contain specific PSPG motifs, and genes in these ten groups have specific tissue expressions. This suggests that the UGT genes in each group could have similar glycosylation roles corresponding to analogous secondary metabolites in alfalfa. Additionally, multiple cis-acting elements found in MsUGT promoter regions, such as phytohormone and flavonoids, indicate that 90 UGT members could be induced by these features, which are also related to secondary metabolism. Therefore, our study identified 90 UGT members inten evolutionary groups that are likely related to glycosylation modifications with secondary metabolites in alfalfa. These findings help uncover pivotal regulatory mechanisms associated with secondary metabolism in plant yield and quality and contribute to genetic modification and breeding in alfalfa and other plant species.

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Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits

Cited by 33 publications

References 79 publications

Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress

Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress

Alfalfa genomic selection for different stress‐prone growing regions

Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa (Medicago sativa L.)

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