Identification and validation of two major QTLs for spike compactness and length in bread wheat (Triticum aestivum L.) showing pleiotropic effects on yield-related traits

Li, Tao; Deng, Guangbing; Su, Yan; Zhao, Yanping; Tang, Yanyan; Wang, Jinhui; Qiu, Xvebing; Pu, Xi; Li, Jun; Liu, Zehou; Zhang, Haili; Liang, Jinsong; Yang, Wuyun; Yu, Maoqun; Wei, Yuming; Long, Hai

doi:10.1007/s00122-021-03918-8

Cited by 37 publications

(37 citation statements)

References 74 publications

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“…Previous studies have found that integrating multiple favorable QTL into the same genetic background can significantly optimize plant traits ( Fan et al, 2019 ; Li et al, 2021 ). This pyramiding effect of multiple loci is an effective means for the improvement of modern wheat varieties.…”

Section: Discussionmentioning

confidence: 99%

“…In order to further excavate major loci associated with spike development among modern wheat varieties, scholars worldwide have identified a large number of QTL for spike traits ( Jantasuriyarat et al, 2004 ; Kumar et al, 2007 ; Ma et al, 2007 ; Cui et al, 2012 ; Zhai et al, 2016 ; Tao et al, 2019 ; Kuang et al, 2020 ; Li et al, 2021 ). For example, Ma et al (2007) analyzed five spike traits in a recombinant inbred line (RIL) population and an immortalized F 2 population.…”

Section: Introductionmentioning

confidence: 99%

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Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

et al. 2021

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Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

et al. 2021

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“…QSc/Sl.cib-2AS , comprising QSc.cib-2AS and QSl.cib-2AS loci, was physically co-localized in the interval of 167.65–183.91 Mb on the short arm of chromosome 2A ( Table 2 ). Comparison analysis revealed that there were 13 loci for SC or/and SL on the chromosome 2AS identified previously, but among them, no major and sable QTL was overlapped or close to QSc/Sl.cib-2AS in the present study ( Yao et al, 2009 ; Zhang et al, 2009 ; Li et al, 2016 , 2019b , 2021a ; Fu et al, 2017 ; Liu et al, 2018 , 2019 ) ( Supplementary Table 13 ). QSc/Sl.cib-2AS showed a significant effect on PHT and GR, but no effect on SNS in our study.…”

Section: Discussionmentioning

confidence: 45%

“…The spike is the reproductive organ of the wheat plant and is an essential component to produce and hold grains ( Faris et al, 2014 ). The morphological traits of a spike, including spike compactness (SC), spike length (SL), and spikelet number per spike (SNS), have been found to be greatly associated with grain yield in previous studies ( Chai et al, 2019 ; Wolde et al, 2019 ; Li et al, 2021a ; You et al, 2021 ). Therefore, the identification of major and stable quantitative trait loci (QTL)/genes for SC and SL is an efficient strategy to cultivate and domesticate high-yield varieties with the ideal plant architecture in wheat for breeders ( Ma et al, 2007 ; Faris et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic Dissection of Three Major Quantitative Trait Loci for Spike Compactness and Length in Bread Wheat (Triticum aestivum L.)

Feng

et al. 2022

Front. Plant Sci.

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Spike compactness (SC) and length (SL) are the components of spike morphology and are strongly related to grain yield in wheat (Triticum aestivum L.). To investigate quantitative trait loci (QTL) associated with SC and SL, a recombinant inbred lines (RIL) population derived from the cross of Bailangmai (BLM, a Tibet landrace) and Chuanyu 20 (CY20, an improved variety) was employed in six environments. Three genomic regions responsible for SC and SL traits were identified on chromosomes 2A and 2D using bulked segregant exome sequencing (BSE-Seq). By constructing genetic maps, six major QTL were repeatedly detected in more than four environments and the best linear unbiased estimation (BLUE) datasets, explaining 7.00–28.56% of the phenotypic variation and the logarithm of the odd (LOD) score varying from 2.50 to 13.22. They were co-located on three loci, designed as QSc/Sl.cib-2AS, QSc/Sl.cib-2AL, and QSc/Sl.cib-2D, respectively. Based on the flanking markers, their interactions and effects on the corresponding trait and other agronomic traits were also analyzed. Comparison analysis showed that QSc/Sl.cib-2AS and QSc/Sl.cib-2AL were possibly two novel loci for SC and SL. QSc/Sl.cib-2AS and QSc/Sl.cib-2D showed pleiotropic effects on plant height and grain morphology, while QSc/Sl.cib-2AL showed effects on spikelet number per spike (SNS) and grain width (GW). Based on the gene annotation, orthologous search, and spatiotemporal expression patterns of genes, TraesCS2A03G0410600 and TraesCS2A03G0422300 for QSc/Sl.cib-2AS, and TraesCS2D03G1129300 and TraesCS2D03G1131500 for QSc/Sl.cib-2D were considered as potential candidate genes, respectively. These results will be useful for fine mapping and developing new varieties with high yield in the future.

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“…Many important agronomic traits in allopolyploid crops are determined by their specific dominant component subgenome(s) (Zohary and Feldman, 1962 ; Eckardt, 2014 ; Hao et al, 2019 ; Cao et al, 2020 ; Li T. et al, 2021 ). In allohexaploid common wheat, the dominant A subgenome often determines inflorescence morphology and growth habit, whereas the D subgenome is related to disease resistance and ecological adaptability (Feldman and Levy, 2009 ).…”

Section: Discussionmentioning

confidence: 99%

Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD)

Zhang

Guo

et al. 2022

Front. Plant Sci.

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Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to “transcriptome shock. ” However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.

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Identification and validation of two major QTLs for spike compactness and length in bread wheat (Triticum aestivum L.) showing pleiotropic effects on yield-related traits

Cited by 37 publications

References 74 publications

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

Genetic Dissection of Three Major Quantitative Trait Loci for Spike Compactness and Length in Bread Wheat (Triticum aestivum L.)

Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD)

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