Natural variation in PTB1 regulates rice seed setting rate by controlling pollen tube growth

Li, Shuangcheng; Li, Wenbo; Huang, Bin; Cao, Xuemei; Zhou, X.D.; Ye, Shumei; Li, Chengbo; Gao, Fengyan; Zou, Ting; Xie, Kailong; Ren, Yun; Ai, Peng; Tang, Yang; Li, Xuemei; Deng, Qi; Wang, Shiquan; Zheng, Aiping; Zhu, Jun; Liu, Huainian; Wang, Lingxia; Li, Ping

doi:10.1038/ncomms3793

Cited by 67 publications

(47 citation statements)

References 52 publications

(49 reference statements)

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“…Henceforth, we combined haplotype (LD)-based high-resolution trait association mapping at target SW-specific QTL region with differential gene expression profiling (during seed development in low and high seed weight parental genotypes), which delineated one regulatory SNP-containing embryo defective protein-coding gene governing seed weight in chickpea. Such haplotype-specific association analysis in presence of high-resolution significant LD at major QTL region have utility to scale-down the QTLs to specific candidate gene(s) regulating important agronomic traits in crop plants106107108109.…”

Section: Discussionmentioning

confidence: 99%

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Kujur

Upadhyaya

Shree

et al. 2015

Sci Rep

101

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We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.

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Section: Discussionmentioning

confidence: 99%

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Kujur

Upadhyaya

Shree

et al. 2015

Sci Rep

101

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“…Similar cases have been reported before. PTB1 , which encodes a RING type E3 ubiquitin ligase in rice, positively regulates panicle seed-setting rate and grain yield by promoting pollen tube growth in the STT [7]. Differently, ptb1 exhibits extreme sterility because all the pollen tubes are blocked in the STT.…”

Section: Discussionmentioning

confidence: 99%

“…The S5 locus contains three tightly linked genes that regulate indica - japonica hybrid fertility [6]. A recent study also showed that defective pollen tube growth in pistil could also cause reduced panicle fertility and seed setting [7]. Despite the tremendous progress, however, our understanding of the genetic control of seed-setting rate in rice still remains very fragmented.…”

Section: Introductionmentioning

confidence: 99%

OsCNGC13 promotes seed-setting rate by facilitating pollen tube growth in stylar tissues

Yang

Wang

et al. 2017

PLoS Genet

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Seed-setting rate is a critical determinant of grain yield in rice (Oryza sativa L.). Rapid and healthy pollen tube growth in the style is required for high seed-setting rate. The molecular mechanisms governing this process remain largely unknown. In this study, we isolate a dominant low seed-setting rate rice mutant, sss1-D. Cellular examination results show that pollen tube growth is blocked in about half of the mutant styles. Molecular cloning and functional assays reveals that SSS1-D encodes OsCNGC13, a member of the cyclic nucleotide-gated channel family. OsCNGC13 is preferentially expressed in the pistils and its expression is dramatically reduced in the heterozygous plant, suggesting a haploinsufficiency nature for the dominant mutant phenotype. We show that OsCNGC13 is permeable to Ca2+. Consistent with this, accumulation of cytoplasmic calcium concentration ([Ca2+]cyt) is defective in the sss1-D mutant style after pollination. Further, the sss1-D mutant has altered extracellular matrix (ECM) components and delayed cell death in the style transmission tract (STT). Based on these results, we propose that OsCNGC13 acts as a novel maternal sporophytic factor required for stylar [Ca2+]cyt accumulation, ECM components modification and STT cell death, thus facilitating the penetration of pollen tube in the style for successful double fertilization and seed-setting in rice.

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“…In Torenia fournieri , Torenia concolor , and Brassica , the LURE peptides from synergid cells are similar defensin-like CRPs, and they play an essential role in pollen tube attraction [31–33]. In monocots, ZmES4 induces rapid pollen tube rupture in maize, and OsPTB1 (POLLEN TUBE BLOCKED 1) promotes pollen tube growth to control the rice seed-setting rate [34, 35]. …”

Section: Introductionmentioning

confidence: 99%

Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils

Zhang

et al. 2017

BMC Plant Biol

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BackgroundIn rice, the pistil is the female reproductive organ, and it consists of two stigmas and an ovary. The stigma is capable of receiving pollen grains and guiding pollen tube growth. The ovary holds the embryo sac, which is fertilized with male gametes to produce seed. However, little is known about the gene function and regulatory networks during these processes in rice.ResultsHere, using the RNA-Seq technique, we identified 3531 stigma-preferential genes and 703 stigma-specific genes within the rice pistils, and we verified 13 stigma-specific genes via qRT-PCR and in situ hybridization. The GO analysis showed that the transport-, localization-, membrane-, communication-, and pollination-related genes were significantly enriched in the stigma. Additionally, to identify the embryo sac-preferential/specific genes within the pistils, we compared a wild-type ovary with a mutant dst (defective stigma) ovary and found that 385 genes were down-regulated in dst. Among these genes, 122 exhibited an ovary-specific expression pattern and are thought to be embryo sac-preferential/specific genes within the pistils. Most of them were preferentially expressed, while 14 of them were specifically expressed in the pistil. Moreover, the rice homologs of some Arabidopsis embryo sac-specific genes, which played essential roles during sexual reproduction, were down-regulated in dst. Additionally, we identified 102 novel protein-coding genes, and 6 of them exhibited differences between the stigma and ovary in rice as determined using RT-PCR.ConclusionsAccording to these rice ovary comparisons, numerous genes were preferentially or specifically expressed in the stigma, suggesting that they were involved in stigma development or pollination. The GO analysis indicated that a dry rice stigma might primarily perform its function through the cell membrane, which was different from the wet stigma of other species. Moreover, many embryo sac-preferential/specific genes within the pistils were identified and may be expressed in female rice gametophytes, implying that these genes might participate in the process of female gametophyte specialization and fertilization. Therefore, we provide the gene information for investigating the gene function and regulatory networks during female gametophyte development and fertilization. In addition, these novel genes are valuable for the supplementation and perfection of the existing transcriptome in rice, which provides an effective method of detecting novel rice genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1004-8) contains supplementary material, which is available to authorized users.

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Natural variation in PTB1 regulates rice seed setting rate by controlling pollen tube growth

Cited by 67 publications

References 52 publications

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

OsCNGC13 promotes seed-setting rate by facilitating pollen tube growth in stylar tissues

Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils

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