Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line

dc.authorid0000-0001-5579-5179
dc.authorid0000-0001-9482-2811
dc.authorid0000-0002-0659-0289
dc.authorid0000-0003-2704-5869
dc.authorid0000-0002-7470-0080
dc.authorid0000-0003-1568-1745
dc.authorid0000-0002-6767-4355
dc.contributor.authorGhourı, Fozia
dc.contributor.authorZhu, Jiani
dc.contributor.authorYu, Hang
dc.contributor.authorWu, Jinwen
dc.contributor.authorBaloch, Faheem Shahzad
dc.contributor.authorLiu, Xiangdong
dc.contributor.authorShahid, Muhammad Qasim
dc.date.accessioned2021-06-23T18:40:06Z
dc.date.available2021-06-23T18:40:06Z
dc.date.issued2019
dc.departmentBAİBÜ, Ziraat Fakültesi, Tarla Bitkileri Bölümüen_US
dc.description.abstractAutotetraploid rice is a new germplasm resource obtained by doubling chromosomes through colchicine treatment. There have been many studies on the reproductive characteristics of autotetraploid rice, but little is known about global DNA variations and reasons for low embryo sac fertility in autotetraploid rice. Therefore, an autotetraploid rice line (T446) was used for resequencing and embryo sac fertility was observed. Whole-genome resequencing data revealed 87,229 SNPs and 11,022 InDels in the genome of T446 versus 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 structural variations and 131 and 128 copy number variations were identified in the autotetraploid and its diploid counterpart, respectively. We detected 140 large-effects SNPs and InDel variants that might be related to the embryo sac fertility of autotetraploid rice, including 10 genes that may be closely associated with the development of the embryo sac. Of these, Os02g0292600 and Os06g0565200 were specifically expressed in the ovary. Mature embryo sac fertility was observed through whole-mount eosin B-staining confocal laser scanning microscopy. Many abnormalities were found in the embryo sac of T446, including embryo sac degeneration, embryo sac without female germ unit, abnormal polar nuclei, and poly-eggs, which, in turn, resulted in low seed set. However, whole-genome polymorphisms and genetic differences were high and exhibited broad prospects for genetic improvement. Genetic mutations in genes associated with embryo sac fertility in polyploid rice require further studies.en_US
dc.identifier.doi10.3906/tar-1901-13
dc.identifier.endpage568en_US
dc.identifier.issn1300-011X
dc.identifier.issn1303-6173
dc.identifier.issue6en_US
dc.identifier.scopus2-s2.0-85076225234en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage554en_US
dc.identifier.trdizinid335788en_US
dc.identifier.urihttps://doi.org/10.3906/tar-1901-13
dc.identifier.urihttps://app.trdizin.gov.tr/makale/TXpNMU56ZzRPQT09
dc.identifier.urihttps://hdl.handle.net/20.500.12491/2964
dc.identifier.volume43en_US
dc.identifier.wosWOS:000502956000006en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakTR-Dizinen_US
dc.institutionauthorBaloch, Faheem Shahzad
dc.language.isoenen_US
dc.relation.ispartofTurkish Journal of Agriculture and Forestryen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectEmbryo Sac Abortionen_US
dc.subjectGenome
dc.subjectPolyploidy
dc.subjectResequencing
dc.subjectSeed Set
dc.titleDeciphering global DNA variations and embryo sac fertility in autotetraploid rice lineen_US
dc.typeArticleen_US

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