Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Chen, Caijin; He, Wenchuang; Nassirou, Tondi Yacouba; Nsabiyumva, Athanase; Dong, Xilong; Adedze, Yawo Mawunyo Nevame; Jiang, Deming

doi:10.1016/j.ejbt.2017.08.001

Cited by 21 publications

(17 citation statements)

References 27 publications

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“…Therefore, we decided to investigate the genetic background of Kabre in more detail and performed a genotyping experiment using different markers discriminating O. sativa and O. glaberrima species (Fig 3). Firstly, SSR marker analysis using the marker RM197 was performed according to Chen et al [23]. Furthermore, the deletion of the PROG1 gene and a deletion nearby this gene were investigated by PCR analysis since they are reported to be reliable species-specific O. glaberrima markers [8] [24].…”

Section: Kabre Has Characteristics Typical For O Sativamentioning

confidence: 99%

CRISPR-mediated accelerated domestication of African rice landraces

et al. 2020

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African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage. OPEN ACCESS Citation: Lacchini E, Kiegle E, Castellani M, Adam H, Jouannic S, Gregis V, et al. (2020) CRISPRmediated accelerated domestication of African rice landraces. PLoS ONE 15(3): e0229782. https://doi.

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Section: Kabre Has Characteristics Typical For O Sativamentioning

confidence: 99%

CRISPR-mediated accelerated domestication of African rice landraces

et al. 2020

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“…Joshi et al ( 2000 ) screened 30 ISSR markers for their polymorphism on 42 genotypes representing 17 wild Oryza species, O. glaberrima and O. sativa , and reported few species-specific ISSRs. Chen et al ( 2017 ) genotyped a total of 53 samples, including O. glaberrima (18) and O. sativa (23), with 33 simple sequence repeat (SSR) markers and reported 10 SSRs that displayed different allelic profiles between the two species. Zhao et al ( 2009 ) genotyped 103 O. rufipogon accessions, 10 O. sativa spp.…”

Section: Introductionmentioning

confidence: 99%

Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

et al. 2018

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Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.Electronic supplementary materialThe online version of this article (10.1007/s11032-018-0885-z) contains supplementary material, which is available to authorized users.

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“…PCR was conducted to analyze the genomic variability of pigmented rice. The set of primers used for the SSR was from Chen and others (Chen et al, 2017), while the Rc gene (KX549256) and the GT gene (XM015777298.2) primers were designed to bind at specific sites (Table S1 at Supplementary Data at https://ojs.ptbioch.edu.pl/ index.php/abp). Fifty microliters of the PCR reaction mix consisted of 25 µL of 2× GoTaq ® Green Master Mix (Promega, Cat.M712), 0.2 µM of each primer, 50 ng/µL genomic DNA, and deionized water.…”

Section: Genomic Analysis Of Pigmented Rice From Java Islandmentioning

confidence: 99%

“…The SSR markers are highly suitable for genetic diversity analysis with high reproducibility (Chen et al, 2013). SSR markers were used to effectively assess the genomic variability of African cultivated and wild-type rice (Chen et al, 2017). Both of these rice populations showed SSR allele polymorphisms that separated them well.…”

Section: Introductionmentioning

confidence: 99%

Black rice cultivar from Java Island of Indonesia revealed genomic, proteomic, and anthocyanin nutritional value

et al. 2021

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Black rice is considered to be functional food containing anthocyanins as bioactive compounds. This study examined the genomic and proteomic patterns in local black rice from Java Island, Indonesia, with attention to the mechanism of anthocyanin synthesis. Three kinds of black rice from Java Island, including black rice from East Java (BREJ), black rice from Central Java (BRCJ), and black rice from West Java (BRWJ), were studied in comparison to white rice (WREJ) and red rice (RREJ). Genomic profiling was done by simple sequence repeat (SSR) analysis, and sequencing of red coleoptile (Rc) and glycosyltransferase (GT) genes, followed by in silico analysis. Total anthocyanin was investigated by ultra-high performance liquid chromatography- diode array detector (UHPLC-DAD). The proteomic profiles were determined by liquid-chromatography and mass spectrometry of tryptic peptides. The SSR profiles showed a specific band in each black rice variant. The Rc gene exon-2 sequences were similar in the three black rice cultivars. The GT gene sequence was identified as a new variant that correlates with the purple stem, leaf, bran, and whole grain morphology seen exclusively in the BRWJ cultivar. The anthocyanin composition in Java black rice is diverse. The highest cyanidin level was seen in BRWJ and the highest level of peonidin-3-O-glucoside in BREJ. Proteomic profiling of the black rice cultivars demonstrated that the expression of proteins that might be related to the levels of anthocyanin synthesis varied. These studies conclude that the genomic, proteomic and anthocyanins composition of Java black rice cultivars may be used the improvement of their functional nutrition values.

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Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Cited by 21 publications

References 27 publications

CRISPR-mediated accelerated domestication of African rice landraces

CRISPR-mediated accelerated domestication of African rice landraces

Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Black rice cultivar from Java Island of Indonesia revealed genomic, proteomic, and anthocyanin nutritional value

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