scholarly journals Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice

2021 ◽  
Vol 22 (2) ◽  
pp. 841
Author(s):  
Nabieu Kamara ◽  
Yamin Jiao ◽  
Zijun Lu ◽  
Kelvin Dodzi Aloryi ◽  
Jinwen Wu ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Bulked Segregant Analysis ◽  
Low Fertility ◽  
High Fertility ◽  
Rna Seq ◽  
Autotetraploid Rice ◽  
Genetic Mechanisms ◽  
New Perspective

Neo-tetraploid rice with high fertility is a useful germplasm for polyploid rice breeding, which was developed from the crossing of different autotetraploid rice lines. However, little information is available on the molecular mechanism underlying the fertility of neo-tetraploid rice. Here, two contrasting populations of tetraploid rice, including one with high fertility (hereafter referred to as JG) and another with low fertility (hereafter referred to as JD), were generated by crossing Huaduo 3 (H3), a high fertility neo-tetraploid rice that was developed by crossing Jackson-4x with 96025-4x, and Huajingxian74-4x (T452), a low fertility autotetraploid rice parent. Cytological, global genome sequencing-based bulked-segregant (BSA-seq) and CRISPR/Cas9 technology were employed to study the genes associated with pollen fertility in neo-tetraploid rice. The embryo sacs of JG and JD lines were normal; however, pollen fertility was low in JD, which led to scarce fertilization and low seed setting. Cytological observations displayed low pollen fertility (25.1%) and approximately 31.3 and 27.2% chromosome lagging at metaphase I and II, and 28.8 and 24.8% chromosome straggling at anaphase I and II in JD, respectively. BSA-seq of F2–3 generations and RNA-seq of F4 generation detected a common fragment, i.e., 18,915,234–19,500,000, at chromosome 7, which was comprised of 78 genes associated with fertility. Among 78 genes, 9 genes had been known to be involved in meiosis and pollen development. Two mutants ny1 (LOC_Os07g32406) and ny2 (LOC_Os07g32040) were generated by CRISPR/Cas9 knockout in neo-tetraploid rice, and which exhibited low pollen fertility and abnormal chromosome behavior. Our study revealed that two unknown genes, LOC_Os07g32406 (NY1) and LOC_Os07g32040 (NY2) play an important role in pollen development of neo-tetraploid rice and provides a new perspective about the genetic mechanisms of fertility in polyploid rice.

scholarly journals Comparative Cytological and Transcriptome Analysis Revealed the Normal Pollen Development Process and Up-Regulation of Fertility-Related Genes in Newly Developed Tetraploid Rice

2020 ◽  
Vol 21 (19) ◽  
pp. 7046
Author(s):  
Jinwen Wu ◽  
Yuanmou Chen ◽  
Hong Lin ◽  
Yang Chen ◽  
Hang Yu ◽  
...  
Keyword(s):  
Pollen Development ◽  
Pollen Fertility ◽  
Development Process ◽  
Low Fertility ◽  
Abnormal Development ◽  
Lower Percentage ◽  
High Fertility ◽  
Rna Seq ◽  
Autotetraploid Rice ◽  
Environmentally Sensitive

Autotetraploid rice is a useful germplasm for polyploid rice breeding; however, low seed setting is a major hindrance for its utilization. Here, we reported the development of a new tetraploid rice, Huoduo1 (H1), which has the characteristic of high fertility, from crossing generations of autotetraploid rice. Cytological observations displayed the high fertility of the pollen (95.62%) in H1, a lower percentage of pollen mother cell (PMC) abnormalities, and stable chromosome configurations during the pollen development process compared with its parents. Using RNA-seq analysis, we detected 440 differentially expressed genes (DEGs) in H1 compared with its parents. Of these DEGs, 193 were annotated as pollen fertility-related genes, and 129 (~66.8%) exhibited significant up-regulation in H1 compared with the parents, including three environmentally sensitive genic male sterility genes (TMS9-1, TMS5, and CSA), one meiosis gene (RAD51D), and three tapetal-related genes (MIL2, OsAP25, and OsAP37), which were validated by qRT-PCR in this study. Two genes, TMS9-1 and TMS5, were knocked out using CRISPR/Cas9 technology, and their mutants displayed low fertility and the abnormal development of pollen. Our findings provide evidence for the regulatory mechanisms of fertility in tetraploid rice and indicated that the up-regulation of pollen fertility-related genes may contribute to the high fertility in new tetraploid rice.

scholarly journals Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice

2020 ◽  
Vol 21 (20) ◽  
pp. 7489
Author(s):  
Zijun Lu ◽  
Xiaotong Guo ◽  
Zhiyu Huang ◽  
Juan Xia ◽  
Xiang Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Expression Patterns ◽  
Middle Layer ◽  
Low Fertility ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
High Fertility ◽  
Autotetraploid Rice

Autotetraploid rice is a useful rice germplasm for polyploid rice breeding. However, low fertility limits its commercial production. A neo-tetraploid rice with high fertility was developed from the progenies of crossing between autotetraploid lines by our research group. Our previous study showed that a myeloblastosis (MYB) transcription factor, MOF1, might be associated with the pollen development in tetraploid rice. However, little information is available about its role in pollen development in tetraploid rice. Here, we identified a new haplotype of MOF1 from neo-tetraploid rice and marked it as MOF1a. Transcriptome and qRT-PCR analysis demonstrated that MOF1a highly expressed in anthers, and displayed differential expression in neo-tetraploid rice compared to tetraploid rice line with low pollen fertility. The mutant (mof1a) of MOF1a, which was generated by CRISPR/Cas9 knockout in neo-tetraploid rice, showed low pollen fertility, and also exhibited abnormal tapetum and middle layer development, and defective chromosome behaviors during meiosis. A total of 13 tapetal related genes were found to be up-regulated in meiotic anthers of MOF1a compared with wild type plants by RNA-seq analysis, including CYP703A3, PTC1, and OsABCG26, which had been demonstrated to affect tapetal development. Moreover, 335 meiosis-related genes displayed differential expression patterns at same stage, including nine important meiosis-related genes, such as metallothionein OsMT1a. These results demonstrated that MOF1a plays an important role in pollen development and provides a foundation for understanding the molecular mechanism underlying MOF1a in reproduction of tetraploid rice.

scholarly journals Comparative cytological and transcriptome analysis reveals high pollen fertility and upregulation of related genes in neo-tetraploid rice

2019 ◽  
Author(s):  
Jinwen Wu ◽  
Yuanmou Chen ◽  
Hong Lin ◽  
Yang Chen ◽  
Hang Yu ◽  
...  
Keyword(s):  
Pollen Development ◽  
Pollen Fertility ◽  
Development Process ◽  
Yield Potential ◽  
Lower Percentage ◽  
High Fertility ◽  
Rice Breeding ◽  
Rna Seq ◽  
High Pollen ◽  
Autotetraploid Rice

Abstract Background: Autotetraploid rice is a useful germplasm for polyploid rice breeding; however, low seed setting is a major hindrance for the utilization of autotetraploid rice. Our previous study demonstrated that neo-tetraploid rice have great yield potential, which is thought to be one effective way to overcome the low fertility of autotetraploid rice. However, there is little known about the cause of high pollen fertility in neo-tetraploid rice. Here, we employed cytology and RNA-seq to study the molecular genetic mechanism of high pollen fertility in neo-tetraploid rice.Results: Cytological observations indicate that H1 displayed high pollen fertility (95.62%), lower percentage of PMC cell abnormalities, and stable chromosome configurations during the pollen development process compared with its two parents. RNA-seq analysis detected 1483 differentially expressed genes (DEGs) in neo-tetraploid rice compared with its two parents. Of these DEGs, 433 were annotated as pollen fertility-related genes, and 240 (~55.4%) exhibited significant upregulation in neo-tetraploid rice compared with its two parents, including nine cloned genes ( CSA , TMS5 etc.) that were validated by qRT-PCR and had been demonstrated to be pollen fertility-related genes. We further selected TMS5 as a candidate gene and analysed its phenotype in neo-tetraploid rice using the CRISPR/Cas9 technique. Significant variations have been detected in phenotypic charts, pollen development process and expression level in H1 and its TMS5 knockout lines.Conclusions: Our finding provides strong evidence for the regulatory mechanisms of neo-tetraploid rice, and upregulation of pollen fertility-related genes should be associated with high fertility. Moreover, the present study provides a new useful germplasm for polyploidy rice breeding.

scholarly journals Comparative cytological and transcriptome analysis reveals high pollen fertility and upregulation of environmentally sensitive genic male sterility genes in neo-tetraploid rice

2020 ◽  
Author(s):  
Jinwen Wu ◽  
Yuanmou Chen ◽  
Hong Lin ◽  
Yang Chen ◽  
Hang Yu ◽  
...  
Keyword(s):  
Male Sterility ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Development Process ◽  
Rice Breeding ◽  
Rna Seq ◽  
High Pollen ◽  
Autotetraploid Rice ◽  
Environmentally Sensitive ◽  
Sterility Genes

Abstract Background: Autotetraploid rice is a useful germplasm for polyploid rice breeding; however, low seed setting is a major hindrance for the utilization of autotetraploid rice. Our previous study demonstrated that neo-tetraploid rice have great yield potential, which is thought to be one effective way to overcome the low fertility of autotetraploid rice. However, there is little known about the cause of high pollen fertility in neo-tetraploid rice. Here, we employed cytology and RNA-seq to study the molecular genetic mechanism of high pollen fertility in neo-tetraploid rice. Results: Cytological observations indicate that H1 displayed high pollen fertility (95.62%), lower percentage of pollen mother cells（PMCs）abnormalities, and stable chromosome configurations during the pollen development process compared with its two parents. RNA-seq analysis detected 1479 differentially expressed genes (DEGs) in neo-tetraploid rice compared with its two parents. Of these DEGs, 433 were annotated as pollen fertility-related genes, and 240 (~55.4%) exhibited significant upregulation in neo-tetraploid rice compared with its two parents, including nine cloned genes ( TMS5 , CSA etc.) that were validated by qRT-PCR and had been demonstrated to be pollen fertility-related genes. We further selected TMS5 as a candidate gene and analysed its phenotype in neo-tetraploid rice using the CRISPR/Cas9 technique. Significant variations have been detected in phenotypic charts, pollen development process and expression level in H1 and TMS5 knockout lines. Conclusion: Our finding provides strong evidence for the regulatory mechanisms of neo-tetraploid rice, and upregulation of pollen fertility-related genes should be associated with high fertility. Moreover, knockout of environmentally sensitive genic male sterility genes in the present study provide the new useful germplasm for polyploidy rice breeding.

scholarly journals Comparative cytological and transcriptome analysis reveals high pollen fertility and upregulation of environmentally sensitive genic male sterility genes in neo-tetraploid rice

2020 ◽  
Author(s):  
Jinwen Wu ◽  
Yuanmou Chen ◽  
Hong Lin ◽  
Yang Chen ◽  
Hang Yu ◽  
...  
Keyword(s):  
Male Sterility ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Development Process ◽  
Rice Breeding ◽  
Rna Seq ◽  
High Pollen ◽  
Autotetraploid Rice ◽  
Environmentally Sensitive ◽  
Sterility Genes

Abstract Background: Autotetraploid rice is a useful germplasm for polyploid rice breeding; however, low seed setting is a major hindrance for the utilization of autotetraploid rice. Our previous study demonstrated that neo-tetraploid rice have great yield potential, which is thought to be one effective way to overcome the low fertility of autotetraploid rice. However, there is little known about the cause of high pollen fertility in neo-tetraploid rice. Here, we employed cytology and RNA-seq to study the molecular genetic mechanism of high pollen fertility in neo-tetraploid rice. Results: Cytological observations indicate that H1 displayed high pollen fertility (95.62%), lower percentage of pollen mother cells（PMCs）abnormalities, and stable chromosome configurations during the pollen development process compared with its two parents. RNA-seq analysis detected 440 differentially expressed genes (DEGs) in neo-tetraploid rice compared with its two parents. Of these DEGs, 193 were annotated as pollen fertility-related genes, and 129 (~66.8%) exhibited significant upregulation in neo-tetraploid rice compared with its two parents, including nine cloned genes ( TMS9-1 , TMS5 etc.) that were validated by qRT-PCR and had been demonstrated to be pollen fertility-related genes. We further selected TMS9-1 and TMS5 as the candidate gene and analysed its pollen fertility in neo-tetraploid rice using the CRISPR/Cas9 technique. Significant variations have been detected in pollen fertility value, pollen development process and expression level in H1 and its knock out lines. Conclusion: Our finding provides strong evidence for the regulatory mechanisms of neo-tetraploid rice, and upregulation of pollen fertility-related genes should be associated with high fertility. Moreover, knockout of environmentally sensitive genic male sterility genes in the present study provides the new useful germplasm for polyploidy rice breeding.

scholarly journals Identification of stable pollen development related reference genes for accurate qRT-PCR analysis and morphological variations in autotetraploid and diploid rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253244
Author(s):  
Jinwen Wu ◽  
Hao Fan ◽  
Yifan Hu ◽  
Haibin Guo ◽  
Hong Lin ◽  
...  
Keyword(s):  
Reference Genes ◽  
Pollen Development ◽  
Pollen Fertility ◽  
Expression Patterns ◽  
Cytochrome B5 ◽  
Development Stages ◽  
Qrt Pcr ◽  
Autotetraploid Rice ◽  
Fertility Genes ◽  
Diploid Rice

Autotetraploid rice exhibited hybrid vigor and greater genetic variation compared to diploid rice, but low pollen fertility is a major hindrance for its utilization. Our previous analysis revealed that large number of pollen fertility genes were exhibited down-regulation in autotetraploid rice. Hence, it is of utmost importance to reveal the expression patterns of pollen fertility genes with high accuracy. To find stable reference genes for autotetraploid rice, we compared the pollen development stages between diploid and autotetraploid rice, and 14 candidate genes were selected based on transcriptome analysis to evaluate their expression levels. Autotetraploid rice (i.e. Taichung65-4x) displayed lower seed set (40.40%) and higher percentage of abnormalities during the pollen development process than its diploid counterpart. To detect the candidate reference genes for pollen development of autotetraploid and diploid rice, we used five different algorithms, including NormFinder, BestKeeper, ΔCt method, geNorm and Re-Finder to evaluate their expression patterns stability. Consequently, we identified two genes, Cytochrome b5 and CPI, as the best candidate reference genes for qRT-PCR normalization in autotetraploid and diploid rice during pre-meiosis, meiosis, single microspore and bicellular pollen development stages. However, Cytochrome b5 was found to be the most stably expressed gene during different pollen development stages in autotetraploid rice. The results of our study provide a platform for subsequent gene expression analyses in autotetraploid rice, which could also be used in other polyploid plants.

ON-FARM FORESTRY DEVELOPMENT OPTIONS FOR NORTHLAND

1986 ◽  
pp. 27-32
Author(s):  
J.S. Clark
Keyword(s):  
Joint Ventures ◽  
Low Fertility ◽  
High Fertility ◽  
Financial Returns ◽  
Farm Forestry ◽  
Hill Country ◽  
Financial Position ◽  
On Farm

Agroforests and woodlots offer Northland hill country farmers investment and diversification opportunities. Agroforests have less effect on the "whole farm" financial position than woodlots, especially where a progressive planting regime is adopted and where no further borrowing is required. Establishment and tending costs for agro-forests are lower, and returns come much sooner. The proven opportunity for continued grazing under trees established in this manner, apart from a short post-planting period, further enhances the agroforesty option. Even where there is reluctance on a farmer's part to plant trees on high fertility land, the expected financial returns from agroforests on low and medium fertility land will increase the overall long-term profitability and flexibility of the whole farming operation. Woodlots may be more appropriate on low fertility areas where weed reversion is likely. Joint ventures may be worth considering where farm finances are a limited factor. Keywords: On-farm forestry development, Northland hill country, agroforestry, woodlots, diversification, joint ventures, progressive planting regimes, grazing availability.

scholarly journals RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Álvaro Figueroa ◽  
Antonio Brante ◽  
Leyla Cárdenas
Keyword(s):  
De Novo ◽  
Juvenile Stage ◽  
Type I ◽  
Rna Seq ◽  
Mrna Synthesis ◽  
De Novo Transcriptome ◽  
Larval Stages ◽  
Divergent Gene ◽  
Genetic Mechanisms ◽  
Planktotrophic Larvae

AbstractThe polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.

Sign in / Sign up

Export Citation Format

Share Document