Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency

Liu, Changying; Qiu, Qingcheng; Zou, Bangxing; Wu, Qi; Ye, Xueling; Wan, Yan; Huang, Jingwei; Wu, Xiaoyong; Sun, Yanxia; Yan, Huiling; Fan, Yu; Jiang, Liangzhen; Zheng, Xin; Zhao, Gang; Zou, Liang; Xiang, Dabing

doi:10.1016/j.plaphy.2023.02.023

Cited by 3 publications

(4 citation statements)

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“…The differences in genome level among the four TB varieties were analyzed by genomic re-sequencing. The genomes of XQ and FH were re-sequenced in our previous study, and 1,716 genes in XQ and 2,428 genes in FH showed genome sequence variation compared with Pinku 1 (reference genome), respectively ( Liu et al, 2023a ). In this study, the genome of YQ1 and YQ2 were analyzed by genomic re-sequencing.…”

Section: Resultsmentioning

confidence: 99%

“…The genome re-sequencing of XQ2 and FH has been determined in our previous study ( Liu et al, 2023a ). In this study, the genomic data of YQ1 and YQ2 was also re-sequenced.…”

Section: Methodsmentioning

confidence: 99%

“…The leaves were immediately frozen in liquid nitrogen and then stored in a −80°C refrigerator for DNA extraction. The methods of DNA extraction, construction of DNA libraries, Illumina sequencing and data processing were similar to those described in our previous study ( Liu et al, 2023a ). The raw data of genomic sequencing was submitted to NCBI Short Read Archive database (accession number: PRJNA980146 ).…”

Section: Methodsmentioning

confidence: 99%

“…The raw data of genomic sequencing was submitted to NCBI Short Read Archive database (accession number: PRJNA980146 ). The genome-wide genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletions (InDels), copy number variations (CNVs) and structure variations (SVs), were examined by comparing the genomes of YQ1 and YQ2 with reference genome sequence of TB, 1 and the genes with genome sequence variation were finally generated ( Liu et al, 2023a ).…”

Section: Methodsmentioning

confidence: 99%

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Interkingdom multi-omics analysis reveals the effects of nitrogen application on growth and rhizosphere microbial community of Tartary buckwheat

Qiu,

Xiang,

et al. 2023

Front. Microbiol.

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Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root–microbe interactions.

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Section: Resultsmentioning

confidence: 99%

“…The genome re-sequencing of XQ2 and FH has been determined in our previous study ( Liu et al, 2023a ). In this study, the genomic data of YQ1 and YQ2 was also re-sequenced.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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