Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line
Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line
Autotetraploid rice is a new germplasm resource obtained by doubling chromosomes through colchicine treatment. Therehave been many studies on the reproductive characteristics of autotetraploid rice, but little is known about global DNA variations andreasons for low embryo sac fertility in autotetraploid rice. Therefore, an autotetraploid rice line (T446) was used for resequencing andembryo sac fertility was observed. Whole-genome resequencing data revealed 87,229 SNPs and 11,022 InDels in the genome of T446versus E246 (diploid rice), which had an average of 23.37 SNPs and 2.95 InDels per 100 kb. A total of 17,375 and 17,171 structuralvariations and 131 and 128 copy number variations were identified in the autotetraploid and its diploid counterpart, respectively. Wedetected 140 large-effects SNPs and InDel variants that might be related to the embryo sac fertility of autotetraploid rice, including10 genes that may be closely associated with the development of the embryo sac. Of these, Os02g0292600 and Os06g0565200 werespecifically expressed in the ovary. Mature embryo sac fertility was observed through whole-mount eosin B-staining confocal laserscanning microscopy. Many abnormalities were found in the embryo sac of T446, including embryo sac degeneration, embryo sacwithout female germ unit, abnormal polar nuclei, and poly-eggs, which, in turn, resulted in low seed set. However, whole-genomepolymorphisms and genetic differences were high and exhibited broad prospects for genetic improvement. Genetic mutations in genesassociated with embryo sac fertility in polyploid rice require further studies.
___
- Alp S, Ercisli S, Dogan H, Temim E, Leto A et al. (2016). Chemical
composition and antioxidant activity Ziziphora clinopodioides
ecotypes from Turkey. Romanian Biotechnological Letters 21:
11298-11303.
- Boeva V, Popova T, Bleakley K, Chiche P, Cappo J et al. (2012).
Control-FREEC: A tool for assessing copy number and allelic
content using next-generation sequencing data. Bioinformatics
28 (3): 423-425.
- Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM et al. (2009).
BreakDancer: An algorithm for high-resolution mapping of
genomic structural variation. Nature Methods 6 (9): 677-681.
- Chen L, Shahid MQ, Wu J, Chen Z, Wang L et al. (2018). Cytological
and transcriptome analyses reveal abrupt gene expression
for meiosis and saccharide metabolisms that associated with
pollen abortion in autotetraploid rice. Molecular Genetics and
Genomics 293: 1407. doi: 10.1007/s00438-018-1471-0
- Chen L, Yuan Y, Wu J, Chen Z, Wang L et al. (2019). Carbohydrate
metabolism and fertility related genes high expression levels
promote heterosis in autotetraploid rice harboring double
neutral genes. Rice 12: 34. doi: 10.1186/s12284-019-0294-x
- Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE et al. (2008).
Evolutionary genetics of genome merger and doubling in
plants. Genetics 42: 443-461.
- Fu CY, Liu WG, Liu DL, Li JH, Zhu MS et al. (2016). Genomewide DNA polymorphism in the indica rice varieties RGD-7S
and Taifeng B as revealed by whole genome re-sequencing.
Genome 59 (3): 197-207.
- Galiana-Belaguer L, Ibanez G, Cebolla-Cornejo J, Rosello S (2018).
Evaluation of germplasm in Solanum section Lycopersicon for
tomato taste improvement. Turkish Journal of Agriculture and
Forestry 42: 309-321. doi: 10.3906/tar-1712-61
- Guo H, Mendrikahy JN, Xie L, Deng JF, Lu ZJ et al. (2017).
Transcriptome analysis of neo-tetraploid rice reveals specific
differential gene expressions associated with fertility and
heterosis. Scientific Reports 10: 40139. doi: 10.1038/srep40139
- Guo HB, Lu YG, Feng JH, Yang B, Liu XD (2006). Further observation
on the formation and development of autotetraploid rice
embryo sac using laser scanning confocal microscopy. Acta
Laser Biology Sinica 15: 111-117 (in Chinese with English
abstract).
- He JH, Shahid MQ, Chen ZX, Cheng XA, Liu XD et al. (2011a).
Abnormal PMC microtubule distribution pattern and
chromosome behavior resulted in low pollen fertility of an
intersubspecific autotetraploid rice hybrid. Plant Systematics
and Evolution 291: 257-265. doi: 10.1007/s00606-010-0386-y
- He JH, Shahid MQ, Li YJ, Guo HB, Cheng XA et al. (2011b). Allelic
interaction of F1
pollen sterility loci and abnormal chromosome
behaviour caused pollen sterility in intersubspecific
autotetraploid rice hybrids. Journal of Experimental Botany
62: 4433-4445. doi: 10.1093/jxb/err098
- Hu CY, Zeng YX, Lu YG, Li JQ, Liu XD (2009). High embryo sac
fertility and diversity of abnormal embryo sacs detected in
autotetraploid indica/japonica hybrids in rice by whole-mount
eosin B-staining confocal laser scanning microscopy. Plant
Breeding 128: 187-192.
- Huang J, Li J, Zhou J, Wang L, Yang S et al. (2018). Identifying a
large number of high-yield genes in rice by pedigree analysis,
whole-genome sequencing, and CRISPR-Cas9 gene knockout.
Proceedings of the National Academy of Sciences of the United
States of America 115 (32): E7559-E7567.
- Huang X, Lu T, Han B (2013) Resequencing rice genomes: an
emerging new era of rice genomics. Trends in Genetics 29 (4):
225-232.
- Huang X, Zhao Y, Wei X, Li C, Wang A et al. (2012). Genome-wide
association study of flowering time and grain yield traits in a
worldwide collection of rice germplasm. Nature Genetics 44:
32-39.
- Jain M, Moharana KC, Shankar R, Kumari R, Garg R (2014). Genome
wide discovery of DNA polymorphisms in rice cultivars with
contrasting drought and salinity stress response and their
functional relevance. Plant Biotechnology Journal 12: 253-264.
- Li H, Durbin R (2009). Fast and accurate short read alignment with
Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
- Li X, Shahid MQ, Wu J, Wang L, Liu X et al. (2016). Comparative
small RNA analysis of pollen development in autotetraploid
and diploid rice. International Journal of Molecular Science
17: 499. doi: 10.3390/ijms17040499
- Li X, Shahid MQ, Xia J, Lu ZJ, Fang N et al. (2017). Analysis of
small RNAs revealed differential expressions during pollen
and embryo sac development in autotetraploid rice. BMC
Genomics 18: 129. doi: 10.1186/s12864-017-3526-8
- Li X, Yu H, Jiao YM, Shahid MQ, Wu JW et al. (2018). Genomewide analysis of DNA polymorphisms, the methylome and
transcriptome revealed that multiple factors are associated
with low pollen fertility in autotetraploid rice. PLoS One 13
(8): e0201854. doi: 10.1371/journal.pone.0201854
- Liu W, Ghouri F, Yu H, Li X, Yu SH et al. (2017). Genome wide resequencing of newly developed rice lines from common wild
rice (Oryza rufipogon Griff.) for the identification of NBSLRR genes. PLoS One 12: e180662. doi: 10.1371/journal.
pone.0180662
- Liu W, Shahid MQ, Bai L, Lu Z, Chen Y et al. (2015). Evaluation of
genetic diversity and development of a core collection of wild
rice (Oryza rufipogon Griff.) populations in China. PLoS One
10 (12): e0145990. doi: 10.1371/journal.pone.0145990
Luan L, Wang X, Long WB, Liu YH, Tu SB et al. (2008). Microsatellite
analysis of genetic variation and population genetic
differentiation in autotetraploid and diploid rice. Biochemical
Genetics 46: 248-266.
- Masterson J (1994). Stomatal size in fossil plants: evidence for
polyploidy in majority of angiosperms. Science 264: 421-424.
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K et al.
(2010). The genome analysis toolkit: a map reduce framework
for analyzing next-generation DNA sequencing data. Genome
Research 20: 1297-1303.
- Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G et
al. (2018). DNA molecular markers in plant breeding: current
status and recent advancements in genomic selection and
genome editing. Biotechnology & Biotechnological Equipment
32: 261-285. doi: 10.1080/13102818.2017.1400401
- Parisod C, Holderegger R, Brochmann C (2010). Evolutionary
consequences of autopolyploidy. New Phytologist 186: 5-17.
Shahid MQ, Chen FY, Li HY, Wang SZ, Chen FF et al. (2013a).
Double-neutral genes, Sa-n and Sb-n, for pollen fertility in rice
to overcome indica × japonica hybrid sterility. Crop Science 53:
164-176. doi: 10.2135/cropsci2012.07.0451
- Shahid MQ, Li YJ, Saleem MF, Wei CM, Naeem M et al. (2013b).
Yield and yield components in autotetraploid and diploid rice
genotypes (indica and japonica) sown in early and late seasons.
Australian Journal of Crop Science 7: 632-641.
- Shahid MQ, Liu GF, Li JQ, Naeem M, Liu XD (2011). Heterosis
and gene action study of agronomic traits in diploid and
autotetraploid rice. Acta Agriculturae Scandinavica Section B -
Soil & Plant Science 61: 23-32.
- Shahid MQ, Sun JF, Wei CM, Zhang P, Liu XD (2010). Studies on the
abnormality of embryo sac and pollen fertility in autotetraploid
rice during different growing seasons. Pakistan Journal of
Botany 42: 7-19.
- Shahid MQ, Xu HM, Lin SQ, Chen ZX, Naeem M et al. (2012).
Genetic analysis and hybrid vigor study of grain yield and
other quantitative traits in autotetraploid rice. Pakistan Journal
of Botany 44: 237-246.
- Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH et al.
(2009). Polyploidy and angiosperm diversification. American
Journal of Botany 96: 336-348.
- Song WC, Zhang YH (1992). Rice tetraploidy and its effect
on agronomic traits and nutritional constituents. Acta
Agronomica Sinica 18: 137-144.
- Subbaiyan GK, Waters DL, Katiyar SK, Sadananda AR, Vaddadi S et
al. (2012). Genome-wide DNA polymorphisms in elite indica
rice inbreds discovered by whole-genome sequencing. Plant
Biotechnology Journal 10: 623-634.
- Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D et
al. (2015). String v10: protein-protein interaction networks,
integrated over the tree of life. Nucleic Acids Research 43 (D1):
D447-D452.
- Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S et al. (2018).
Genomic variation in 3,010 diverse accessions of Asian
cultivated rice. Nature 557: 43-49.
- Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS et al. (2019).
Transcriptome analysis and annotation: SNPs identified from
single copy annotated unigenes of three polyploid blueberry
crops. PLoS One 14 (4): e0216299.
- Wu J, Chen L, Shahid MQ, Chen M, Dong Q et al. (2017). Pervasive
interactions of Sa and Sb loci cause high pollen sterility and
abrupt changes in gene expression during meiosis that could be
overcome by double neutral genes in autotetraploid rice. Rice
10: 49. doi: 10.1186/s12284-017-0188-8
- Wu JW, Hu CY, Shahid MQ, Guo HB, Zeng YX et al. (2013). Analysis
on genetic diversification and heterosis in autotetraploid rice.
Springer Plus 2: 1-12.
- Wu JW, Shahid MQ, Chen L, Chen M, Dong Q et al. (2015).
Polyploidy enhances F1
pollen sterility loci interactions
that increase meiosis abnormalities and pollen sterility in
autotetraploid rice. Plant Physiology 169: 2700-2717. doi:
10.1104/pp.15.00791
- Wu JW, Shahid MQ, Guo HB, Yin W, Chen Z et al. (2014). Comparative
cytological and transcriptomic analysis of pollen development
in autotetraploid and diploid rice. Plant Reproduction 27: 181-
196. doi:10.1007/s00497-014-0250-2
- Yaldız G, Çamlıca M, Nadeem MA, Nawaz MA, Baloch FS (2018).
Genetic diversity assessment in Nicotiana tabacum L. with
iPBS-retrotransposons. Turkish Journal of Agriculture and
Forestry 42: 154-164. doi:10.3906/tar-1708-32
- Yamamoto N, Garcia R, Suzuki T, Solis CA, Tada Y et al. (2018).
Comparative whole genome re-sequencing analysis in upland
New Rice for Africa: insights into the breeding history and
respective genome compositions. Rice 11: 33.
- Yu H, Shahid MQ, Li R, Li W, Liu W et al. (2018). Genome-wide
analysis of genetic variations and the detection of rich variants
of NBS-LRR encoding genes in common wild rice lines. Plant
Molecular Biology Reporter 36: 618-630.
- Zhang L, Cheng Z, Qin R, Qiu Y, Wang JL et al. (2012). Identification
and characterization of an epi-allele of FIE1 reveals a regulatory
linkage between two epigenetic marks in rice. Plant Cell 24:
4407-4421.
- Zhang LM, Luo H, Liu ZQ, Zhao Y, Luo JC et al. (2014). Genomewide patterns of large-size presence/absence variants in
sorghum. Journal of Integrative Plant Biology 56: 24-37.
- Zheng LY, Guo XS, He B, Sun LJ, Peng Y et al. (2011). Genomewide patterns of genetic variation in sweet and grain sorghum
(Sorghum bicolor). Genome Biology 12: R114.
- Zhang P, Zhong K, Shahid MQ, Tong H (2016). Association analysis
in rice: from application to utilization. Frontiers in Plant
Science 7: 1202. doi: 10.3389/fpls.2016.01202