An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

Daware, Anurag; Das, Satyajit; Srivastava, Ram; Badoni, Saurabh; Singh, Ashok Kumar; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

doi:10.3389/fpls.2016.01535

Cited by 27 publications

(15 citation statements)

References 86 publications

(148 reference statements)

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“…The identification of repressors even in transcriptional regulatory proteins, in both rice and Arabidopsis, points to the relevance of this motif in conferring functional properties [3,41]. Since repressors are important for reproductive development of the plant [8,9,10,11,12,13,28,34] and we have been examining the developmental biology of the rice seed [35,42,43,44], the expression of the rice DLN repressors was studied in five stages of rice seed development [35], with respect to four vegetative controls by microarray analysis [44]. There was significant up- and downregulation of 27 and 18 genes, respectively, whose encoded protein had a DLN repressor motif.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Rice Proteins with DLN Repressor Motif/S

Singh

Mathew

Verma

et al. 2019

IJMS

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Transcriptional regulation includes both activation and repression of downstream genes. In plants, a well-established class of repressors are proteins with an ERF-associated amphiphilic repression/EAR domain. They contain either DLNxxP or LxLxL as the identifying hexapeptide motif. In rice (Oryza sativa), we have identified a total of 266 DLN repressor proteins, with the former motif and its modifications thereof comprising 227 transcription factors and 39 transcriptional regulators. Apart from DLNxxP motif conservation, DLNxP and DLNxxxP motifs with variable numbers/positions of proline and those without any proline conservation have been identified. Most of the DLN repressome proteins have a single DLN motif, with higher relative percentage in the C-terminal region. We have designed a simple yeast-based experiment wherein a DLN motif can successfully cause strong repression of downstream reporter genes, when fused to a transcriptional activator of rice or yeast. The DLN hexapeptide motif is essential for repression, and at least two “DLN” residues cause maximal repression. Comparatively, rice has more DLN repressor encoding genes than Arabidopsis, and DLNSPP motif from rice is 40% stronger than the known Arabidopsis SRDX motif. The study reports a straightforward assay to analyze repressor activity, along with the identification of a strong DLN repressor from rice.

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Section: Resultsmentioning

confidence: 99%

Analysis of Rice Proteins with DLN Repressor Motif/S

Singh

Mathew

Verma

et al. 2019

IJMS

Self Cite

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“…QTL-seq has been extensively used for rapid identification of causal SNPs and genes in several crops. In rice, QTL-seq identified candidate genes regulating grain weight, grain length, Pi65(t), a novel broad spectrum resistance gene to rice blast, novel QTLs qDTH4.5 and qDTH6.3 conferring late heading under short-day conditions ( Takagi et al, 2013 ; Daware et al, 2016 ; Ogiso-Tanaka et al, 2017 ; Yaobin et al, 2018 ). Furthermore, QTL-seq coupled with RNA-seq at the bud burst stage in rice enabled identification of a major QTL and candidate gene for salt tolerance ( Lei et al, 2020 ).…”

Section: Novel Trait Mapping Approachesmentioning

confidence: 99%

Genomic resources in plant breeding for sustainable agriculture

Thudi

Ramesh

Schnable

et al. 2021

Journal of Plant Physiology

121

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Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965−85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.

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“…The development of genome databases makes it easy to do QTL analysis by BSA (QTL-seq) in major crops and model plant species, such as rice, barley, and Arabidopsis [18][19][20]. By WGS in buckwheat, we developed the BGDB [11], but its small scaffold size so far prevents its use in QTL-seq analysis.…”

Section: Rapid Construction Of Genetic Maps In Buckwheatmentioning

confidence: 99%

Targeted amplicon sequencing + next-generation sequencing–based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)

et al. 2021

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Background Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines. However, genetic loci and selection markers associated with PHS in buckwheat have not been reported. Results By next-generation sequencing (NGS) of whole-genome of parental lines, we developed a genome-wide set of 300 markers. By NGS- based bulked segregant analysis (NGS-BSA), we developed 100 markers linked to PHS tolerance. To confirm the effectiveness of marker development from NGS-BSA data, we developed 100 markers linked to the self-compatibility (SC) trait from previous NGS-BSA data. Using these markers, we developed genetic maps with AmpliSeq technology, which can quickly detect polymorphisms by amplicon-based multiplex targeted NGS, and performed quantitative trait locus (QTL) analysis for PHS tolerance in combination with NGS-BSA. QTL analysis detected two major and two minor QTLs for PHS tolerance in a segregating population developed from a cross between the PHS-tolerant ‘Kyukei 29’ and the self-compatible susceptible ‘Kyukei SC7’. We found different major and minor QTLs in other segregating populations developed from the PHS-tolerant lines ‘Kyukei 28’ and ‘NARO-FE-1’. Candidate markers linked to PHS developed by NGS-BSA were located near these QTL regions. We also investigated the effectiveness of markers linked to these QTLs for selection of PHS-tolerant lines among other segregating populations. Conclusions We efficiently developed genetic maps using a method combined with AmpliSeq technology and NGS-BSA, and detected QTLs associated with preharvest sprouting tolerance in common buckwheat. This is the first report to identify QTLs for PHS tolerance in buckwheat. Our marker development system will accelerate genetic research and breeding in common buckwheat.

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An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

Cited by 27 publications

References 86 publications

Analysis of Rice Proteins with DLN Repressor Motif/S

Analysis of Rice Proteins with DLN Repressor Motif/S

Genomic resources in plant breeding for sustainable agriculture

Targeted amplicon sequencing + next-generation sequencing–based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)

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