QTL mapping for nitrogen use efficiency and agronomic traits at the seedling and maturity stages in wheat

Zhang, Mingxia; Gao, Mingyang; Zheng, Honghua; Yuan, Yuanyuan; Zhou, Xiuwen; Guo, Ying; Zhang, Guizhi; Zhao, Yan; Kong, Fanmei; An, Yanrong; Li, Sishen

doi:10.1007/s11032-019-0965-8

Cited by 38 publications

(31 citation statements)

References 66 publications

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“…Thus, these highly expressed YTH genes in the wheat spikes might function in the development and architecture of spikes. The selection and creation of wheat germplasm with tolerance to multiple abiotic and biotic stresses is a key challenge for wheat breeding [42][43][44][45][46][47][48][49][50][51][52][53][54][55][56]. Our results and those of previous studies reveal that the expression of YTH gene is involved in the responses to various stresses and in plant development [10,13,15,17,21].…”

Section: Discussionsupporting

confidence: 64%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

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Background: N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RNA binding proteins that affect the fate of m6A-containing RNA by binding m6A. Little is known about the YTH genes in common wheat (Triticum aestivum L.), one of the most important crops for humans. Results: A total of 39 TaYTH genes were identified in common wheat, which are comprised of 13 homologous triads, and could be mapped in 18 out of the 21 chromosomes. A phylogenetic analysis revealed that the TaYTHs could be divided into two groups: YTHDF (TaDF) and YTHDC (TaDC). The TaYTHs in the same group share similar motif distributions and domain organizations, which indicates functional similarity between the closely related TaYTHs. The TaDF proteins share only one domain, which is the YTH domain. In contrast, the TaDCs possess three C3H1-type zinc finger repeats at their N-termini in addition to their central YTH domain. In TaDFs, the predicated aromatic cage pocket that binds the methylysine residue of m6A is composed of tryptophan, tryptophan, and tryptophan (WWW). In contrast, the aromatic cage pocket in the TaDCs is composed of tryptophan, tryptophan, and tyrosine (WWY). In addition to the general aspartic acid or asparagine residue used to form a hydrogen bond with N 1 of m6A, histidine might be utilized in some TaDFb proteins. An analysis of the expression using both online RNA-Seq data and quantitative real-time PCR verification revealed that the TaDFa and TaDFb genes are highly expressed in various tissues/organs compared with that of TaDFcs and TaDCs. In addition, the expression of the TaYTH genes is changed in response to various abiotic stresses. Conclusions: In this study, we identified 39 TaYTH genes from common wheat. The phylogenetic structure, chromosome distribution, and patterns of expression of these genes and their protein structures were analyzed. Our results provide a foundation for the functional analysis of TaYTHs in the future.

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Section: Discussionsupporting

confidence: 64%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

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Section: Methodsmentioning

confidence: 99%

“…After grinding, the plant total nitrogen contents were determined by digestion of H 2 SO 4 -H 2 O and the micro-Kjeldahl method. The calculation methods for the nitrogen use efficiency (NUE) and nitrogen agronomic efficiency (NAE) were those described by Zhang 34 , 35 . NUE (%) = (cumulative plant N uptake from N treatment- cumulative plant N uptake from no-N treatment)/the amount of N fertilizer applied × 100%; NAE (kg N kg -1 ) = (the seed yield in the N treatment-the seed yield in the no-N treatment)/the amount of N fertilizer applied; Net profit ($ ha -1 year -1 ) = the seed yield × cotton price-fertilizer costs-other costs-labor costs.…”

Section: Methodsmentioning

confidence: 99%

Effects of controlled-release urea combined with fulvic acid on soil inorganic nitrogen, leaf senescence and yield of cotton

Geng

Yang

Xian-qi

et al. 2020

Sci Rep

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A split-plot field experiment was conducted in 2018–2019 to study the effects of nitrogen fertilizer types and fulvic acid (FA) rates on soil nitrogen and cotton growth. The nitrogen fertilizers included controlled-release urea (CRU) and urea, which were applied combined with three FA rates (90, 180 and 270 kg ha-1). The main plot was the nitrogen fertilizer type, and the subplot was the FA rate. The results showed that the lint yield of the FA180 treatment was 5.2–8.6% higher than the FA90 and FA270 treatments. Moreover, moderate FA application markedly improved the cotton leaf SPAD value (chlorophyll relative value), photosynthesis and chlorophyll fluorescence parameters compared with low and high FA rates. Replacing urea with CRU significantly increased the soil inorganic nitrogen and nitrogen use efficiency and also improved cotton fiber quality parameters. Meanwhile, the boll weight and seed yield of the CRU treatments were 1.5–8.4% and 3.3–19.1% higher, respectively, than the urea treatments. The interaction between nitrogen type and FA rate had a positive effect on cotton growth. Thus, the application of CRU combined with 180 kg ha-1 FA on cotton can not only improve the fiber quality and delay leaf senescence but also increase the yield and economic benefit.

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“…In other cases, QTLs contained homeologs or paralogs of these high confidence candidates, or previous studies had reported associations to a genetic map using marker data, but not firmly anchored these locations on the reference genome assembly (low confidence co-localisation, n=10). We checked six high confidence candidate loci with annotated reference genome locations (RHT-1 [38], RHT-2 [39], WAPO-A1 [40], ALI-1 [41], TaMyb10-B1 [42], Yr7/Yr5/YrSP [37], PPD-D1 [43]), all of which were within our mapping intervals. We created a genotype-phenotype map for community use by placing all QTLs on the physical map (Supplementary Table 7) to a median interval of 9.2Mb.…”

Section: Phenotypic Characterisation and Qtl Mappingmentioning

confidence: 99%

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

Scott¹,

Fradgley

Bentley

et al. 2020

Preprint

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BackgroundBreeding has helped improve bread wheat yield significantly over the last century. Understanding the potential for future crop improvement depends on relating segregating genetic variation to agronomic traits.ResultsWe bred NIAB Diverse MAGIC population, comprising over 500 recombinant inbred lines, descended from sixteen bread wheat varieties released between 1935-2004. We sequenced the founders’ exomes and promotors by capture. Despite being highly representative of North-West European wheat and capturing 73% of global polymorphism, we found 89% of genes contained no more than three haplotypes. We sequenced each line with 0.3x coverage whole-genome sequencing, and imputed 1.1M high-quality SNPs that were over 99% concordant with array genotypes. Imputation accuracy remained high at coverage as low as 0.076x, with or without the use of founder genomes as reference panels. We created a genotype-phenotype map for 47 traits over two years. We found 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Outside of these loci most traits are polygenic, as revealed by multi-locus shrinkage modelling.ConclusionsHistorically, wheat breeding has reshuffled a limited palette of haplotypes; continued improvement will require selection at dozens of loci of diminishing effect, as most of the major loci we mapped are known. Breeding to optimise one trait generates correlated trait changes, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break critical unfavourable trait-trait associations. Finally, low coverage whole genome sequencing of bread wheat populations is an economical and accurate genotyping strategy.

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QTL mapping for nitrogen use efficiency and agronomic traits at the seedling and maturity stages in wheat

Cited by 38 publications

References 66 publications

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Effects of controlled-release urea combined with fulvic acid on soil inorganic nitrogen, leaf senescence and yield of cotton

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

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