Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice

Peng, Youlin; Gao, Zhenyu; Zhang, Bin; Liu, Chaolei; Xu, Jie; Ruan, Banpu; Hu, Jiang; Guo, Longbiao; Liang, Guohua; Qian, Qian

doi:10.1007/s00299-014-1661-0

Cited by 26 publications

(23 citation statements)

References 26 publications

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“…For instance, D88 and WSL preferred the intronic poly(A) sites in indica but 3′ UTR sites in japonica (Figure a, Table S7). D88, encoding a putative esterase, negatively regulates tiller number, rice shoot branching and panicle structure via the strigolactone signal transduction pathway (Gao et al ., ; Peng et al ., ; Zhao et al ., ). WSL is characterized as a nuclear‐encoded plastid RNA splicing factor that affects chloroplast development and responds to ABA, sugar and salinity stresses by regulating the splicing of chloroplast transcript rpl2 (Tan et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Zhou

Yang

et al. 2019

The Plant Journal

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Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3 0 untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.

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Section: Discussionmentioning

confidence: 99%

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Zhou

Yang

et al. 2019

The Plant Journal

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“…Telah dilaporkan gen Dwarf 88 (D88)/Dwarf 14 (D14) mengatur tinggi tanaman dan jumlah anakan. Namun, gen D88/D14 tidak hanya mengatur anakan, tetapi juga mempengaruhi struktur malai (Peng et al, 2014). Gen MONOCULM 1 (MOC1) merupakan gen yang penting dalam mengontrol anakan padi.…”

Section: Heritabilitas Karakter Malaiunclassified

Keragaman Malai Anakan dan Hubungannya dengan Hasil Padi Sawah (Oryza sativa)

Sutoro¹,

Suhartini²,

Setyowati³

et al. 2016

BPN

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Morpho-physiological and yield components of rice are important character that affect the crop yield potential. Seeds as a sink of crops, its yield are very much determined by the panicle yield components, one of which is various type of tillers. The purpose of the research was to study the variability of panicle types andtheir relationshipwith grain yield of rice. Thirty rice varieties/lines were planted and observed in experimental pots. The study revealed that there are differencesin total number of panicle among varieties or lines. Average number of panicle ranges from 20-50 panicle. Among varieties, there were also differences in total number of panicles grown from primary, secondary, tertiary and quarterly tillers. The number of empty seeds of the panicles increases in the order of the sequences of tiller emergence, i.e., main panicle (11%), primary (12%), secondary (12%), tertiary (16%) and quartery (22%). High yielding rice could be obtained through the development of varieties or cultivation techniques that enable the crops produce more panicle in primary and secondary tillers compare to that in tertiary and quarterly tillers.Keywords: rice, panicle, variability. ABSTRAKKarakter morfofisiologi dan komponen hasil merupakan karakteristik tanaman yang mempengaruhi produktivitas. Hasil biji sebagai salah satu bagian dari sink tanaman ditentukan oleh komponen hasil, di antaranya malai yang berasal dari berbagai tipe/ jenis anakan padi. Tujuan penelitian ini untuk mengetahui keragaman malai anakan dan hubungannya dengan hasil padi. Percobaan dilaksanakan dengan menanam 30 varietas/galur pada pot percobaan. Hasil analisis menunjukkan perbedaan jumlah total malai di antara varietas/galur yang diuji. Jumlah malai berkisar antara 20-50 buah. Di antara varietas yang diuji juga terdapat perbedaan yang nyata pada jumlah malai yang berasal dari anakan primer, sekunder, tersier, dan kuarter. Kehampaan gabah dari setiap jenis malai cenderung meningkat menurut urutan pemunculan malai anakan padi, dimulai dari malai tanaman induk (11%), primer (12%), sekunder (12%), tersier (16%), dan kuarter (22%). Tanaman padi yang dapat memberi hasil tinggi dapat diperoleh melalui perakitan varietas atau teknik budi daya yang dapat menghasilkan terutama malai anakan primer dan sekunder yang relatif banyak dan sedikit atau tanpa anakan tersier dan kuarter.Kata kunci: padi, malai, keragaman.

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“…The mean panicle length for Indonesian rice landraces was 24.1, in which Ketan Mayang had the longest panicle length (35.7 cm). Peng et al (2014) reported that panicle structure is one of the most important factors for rice yield and panicle branches and their number affects spikelet number. Dense panicle structure has been a major target for improvement of rice grain yield because of its relationship with grain number.…”

Section: Agro-morphological Characteristicmentioning

confidence: 99%

GENETIC DIVERSITY AND TRAIT ASSOCIATION ANALYSIS OF INDONESIAN RICE (Oryza sativa L.) GERMPLASM USING SSR MARKERS

Fatimah

Herlina²,

Silitonga³

2017

BIOTROPIA

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Generating a new crop variety with certain desirable traits requires germplasm collection with wide genetic diversity to facilitate accelerated development of improved cultivars. This study was conducted to characterize genetic diversity of Indonesian rice accessions using SSR markers and their agro-morphological characters to allow the identification of Marker Trait Association (MTA). A survey of genetic diversity among 72 traditional landraces of 15 provinces in Indonesia and 24 improved varieties was conducted using four multiplex panels of 14 fluorescent-labeled SSR markers and 22 agro-morphological characters. A total of 140 alleles with an average of 10 alleles per locus and Polymorphism Information Content (PIC) values at 0.73. The population structure identified five subgroups. A total of 4 highly significant MTA were identified. One character with highly significant MTA was number of panicle associated with RM277. Based on SSR marker, RM105 had two MTAs for auricle color and ligule shape. After validation, these MTAs may be deployed to improve rice productivity.

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Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice

Cited by 26 publications

References 26 publications

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Keragaman Malai Anakan dan Hubungannya dengan Hasil Padi Sawah (Oryza sativa)

GENETIC DIVERSITY AND TRAIT ASSOCIATION ANALYSIS OF INDONESIAN RICE (Oryza sativa L.) GERMPLASM USING SSR MARKERS

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