Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204

Shi, Xiaoli; Cui, Fa; Han, Xinyin; He, Yilin; Zhao, Long; Zhang, Na; Zhu, Haidong; Liu, Zhexin; Ma, Bin; Zheng, Shusong; Zhang, Wei; Li, Jiajia; Fan, Xiaoqin; Si, Yaoqi; Tian, Shuiquan; Niu, Jianqing; Wu, Huilan; Liu, Xuemei; Chen, Zhuo; Meng, Deyuan; Zhang, Hao; Wang, Xiaoyan; Song, Liqiang; Sun, Lijing; Han, Jie; Zhao, Hui; Ji, Jun; Wang, Zhiguo; He, Xiaoyu; Li, Ruilin; Chi, Xuebin; Liang, Chengzhi; Niu, Beifang; Xiao, Jun; Li, Junming; Ling, Hong‐Qing

doi:10.1016/j.molp.2022.07.008

Cited by 59 publications

(77 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We previously compared the expression profiles of 44 NRT2 and 217 NPF genes in the roots of KN9204 and J411 cultivated hydroponically with and without N supply and found that up to 79.2% and 43.7% of the root-expressed NRT2 and NPF genes, respectively, displayed differential expression between KN9204 and J411. Under NN conditions, more than two-thirds of the differentially expressed NRT2 and NPF genes exhibited higher expression in KN9204 than in J411, but the proportion of NRT2 and NPF genes with higher expression levels in KN9204 decreased under LN treatment, as the upregulated expression levels of most nitrate transporter genes, NRT2 family in particular, were higher in J411 than in KN9204 ( Shi et al., 2022 ). Similarly, two high-affinity NRT genes ( TraesCS6B02G044300 and TraesCS6D02G035900 ) exhibited lower expression levels in the NIL J411 under NN condition, but higher expression levels in the NIL J411 than in the NIL KN9204 under LN condition ( Table 1 ).…”

Section: Discussionmentioning

confidence: 95%

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Zhi

Zhang

et al. 2022

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for the increased yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), essentially contributes to an improved root system in wheat. To further analyze the biological functions of QMrl-7B in root development, two sets of Triticum aestivum near-isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) named NILKN9204 and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411) named NILJ411, were subjected to transcriptomic analysis. Among all the mapped genes analyzed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that mainly include NO3− transporters, phytohormone signaling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this study, 4308 and 2463 were specifically expressed in the NILKN9204 and NILJ411, respectively. These DEGs reflect different responses of the two sets of NILs to varying N supplies, which likely involve LN-induced root growth. These results explain the better-developed root system and increased root vitality conferred by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

show abstract

Section: Discussionmentioning

confidence: 95%

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Zhi

Zhang

et al. 2022

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Kenong 9204 (KN9204) is a representative winter wheat cultivar widely grown in north China plain, characterized by semi-dwarf (∼ 74 cm), compact plant architecture (∼27,5000 fertile spikes ha -1 ), high yield (∼ 7,500 Kg ha -1 ), and high nitrogen use efficiency (NU P E≈65%, NU T E≈35%) (Shi et al, 2022; Cui et al, 2016; Jia et al, 2006). Dozens of cultivars derived from KN9204 with improved grain yield, overwintering ability, heat resistance and milling quality have been authorized ( Figure 1A ) (Zhao et al, 2015; Li et al, 2021b).…”

Section: Resultsmentioning

confidence: 99%

“…The common wheat is an allohexaploid species with three subgenome ((Ramí rez-Gonzá lez et al, 2018;Shi et al, 2022). Most synteny-pair homologous genes are functionally redundant, with some homologous genes differentiate in expression pattern and function (Ramí rez-Gonzá lez et al, 2018).…”

Section: Identification Of Gene-index Mutations In Kn9204 Mutant Librarymentioning

confidence: 99%

“…The raw sequence data of RNA-seq and ATAC-seq reported in this study have been deposited in the Genome Sequence Archive (Chen et al, 2021a) under accession number CRA009130, in National Genomics Data Center (CNCB-NGDC Members and Partners, 2022), China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences that are publicly accessible at https://ngdc.cncb.ac.cn/gsa. The published RNA-seq and epigenomic data of KN9204 used for analysis is download from CNCB-NGDC under accession number CRA008877 (spike related data, Lin et al 2022) and PRJCA004416 (leaf and root related data, Shi et al 2022).…”

Section: Data Availabilitymentioning

confidence: 99%

See 1 more Smart Citation

Boosting wheat functional genomics via indexed EMS mutant library of KN9204

Wang

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

A better understanding of wheat functional genomics could facilitate the targeted breeding for agronomic traits improvement and environmental adaptation. With the release of reference genomes and extensive re-sequencing data of wheat and relatives, wheat functional genomics enters a new era. However, limited transformation efficiency in wheat hampers in-depth gene functional study and genetic manipulation for breeding. Here, we generated an EMS mutagenesis library of KN9204, a widely grown elite wheat variety in northern China, with available reference genome, transcriptome, and epigenome of various tissues. The library harbors enormous developmental diversity covering important tissues and transition stages. Exome capture sequencing of 2,090 mutant lines, with probes designed by KN9204 genome, revealed that 98.79% of coding genes have mutations and 1,383 EMS-type SNPs per line averagely. Novel allelic variations for important agronomic trait-related genes, such as Rht-D1, Q, TaTB1, and WFZP, were identified. We tested 100 lines with severe mutations in 80 NAC TFs under drought and salinity stresses, and found 13 lines with altered sensitivity. Three lines were further analyzed for the regulation insight of NAC TFs in stress response by combing transcriptome and available chromatin accessibility data. Hundreds of direct targets of NAC with altered transcriptional pattern in mutant lines under salt or drought stress induction were identified, including SNAC1, DREB2B, CML16 and ZFP182, knowing factors in abiotic stresses response. Thus, we have generated and indexed KN9204 EMS mutant library which would facilitate functional genomics study and provide resources for genetic manipulation in wheat.

show abstract

“…The release of the hexaploid wheat reference genome has significantly accelerated the cloning of important QTL candidate genes [ 42 , 43 , 44 ]. In the current study, the stable QTL QScn.cas-3D.2 , were located between the interval AX-110834607 – AX-89337262 .…”

Section: Discussionmentioning

confidence: 99%

Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.)

Liu

Shi

et al. 2022

BMC Plant Biol

View full text Add to dashboard Cite

Background Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross ‘PuBing3228 × Gao8901’ (PG-RIL) and to evaluate the potential values of these QTL to improve yield. Results In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58–25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population. Conclusions Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.

show abstract

Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204

Cited by 59 publications

References 53 publications

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Boosting wheat functional genomics via indexed EMS mutant library of KN9204

Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.)

Contact Info

Product

Resources

About