SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza

Marathi, Balram; Ramos, Joie; Hechanova, Sherry Lou; Oane, R.; Jena, Kshirod K.

doi:10.1007/s10681-014-1213-2

Cited by 29 publications

(23 citation statements)

References 49 publications

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“…In nature, the TSSL in Oryza ranges from 1.25 to 3.21 mm (Kato and Namai, 1987; Li et al ., 2010; Marathi et al ., 2015). Thirteen quantitative trait loci (QTLs) for TSSL have been identified, and are distributed on chromosomes 1, 2, 3, 4, 6, and 7 (Liu et al ., 2015; Marathi et al ., 2015; Dang et al ., 2016). These QTLs explain phenotypic variance ( R 2 ) of 2.9–20.0%; 9 of the 13 QTLs have an R 2 > 10%.…”

Section: Introductionmentioning

confidence: 99%

“…The STL in Oryza ranges from 0.55 to 2.3 mm (Virmani and Athwal, 1973; Uga et al ., 2010). To date, 32 QTLs have been detected for STL, including 1, 1, 12, 3, 3, 3, 2, 0, 3, 2, 0, and 2 on chromosomes 1 to 12, respectively (Uga et al ., 2003, 2010; Yan et al ., 2009; Li et al ., 2010; Marathi et al ., 2015; Dang et al ., 2016). The R 2 of these QTLs ranges from 2.2% to 30.8%; 10 of the 32 QTLs have an R 2 > 10%.…”

Section: Introductionmentioning

confidence: 99%

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OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

et al. 2020

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Stigma characteristics are important factors affecting the seed yield of hybrid rice per unit area. Natural variation of stigma characteristics has been reported in rice, but the genetic basis for this variation is largely unknown. We performed a genome-wide association study on three stigma characteristics in six environments using 1.3 million single-nucleotide polymorphism (SNPs) characterized in 353 diverse accessions of Oryza sativa. An abundance of phenotypic variation was present in the three stigma characteristics of these collections. We identified four significant SNPs associated with stigma length, 20 SNPs with style length (SYL), and 17 SNPs with the sum of stigma and style length, which were detected repeatedly in more than four environments. Of these SNPs, 28 were novel. We identified two causal gene loci for SYL, OsSYL3 and OsSYL2; OsSYL3 was co-localized with the grain size gene GS3. The SYL of accessions carrying allele OsSY-L3 AA was significantly longer than that of those carrying allele OsSYL3 CC. We also demonstrated that the outcrossing rate of female parents carrying allele OsSYL2 AA increased by 5.71% compared with that of the isogenic line carrying allele OsSYL2 CC in an F 1 hybrid seed production field. The allele frequencies of OsSY-L3 AA and OsSYL2 AA decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement in stigma characteristics of parents of hybrid rice.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

et al. 2020

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“…These germplasm has to be exploited in depth to find suitable tolerance source and to further use it in rice breeding. There are 22 wild species in the rice genus along with two cultivated rice ( Marathi et al, 2014 ). Around 4,370 accessions of wild species are available at the gene bank of IRRI and are grouped into 11 different genome types (AA, BB, CC, BBCC, CCDD, EE, FF, GG, HHJJ, HHKK, and KKLL) ( Jena, 2010 ; Sanchez et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

et al. 2018

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Cultivated rice (Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+ exclusion mechanism in root which removes Na+ from the xylem stream by membrane Na+ and K+ transporters, and resulted in low Na+ accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild Oryza species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species (O. alta, O. latifolia, and O. coarctata) and four species (O. rhizomatis, O. eichingeri, O. minuta, and O. grandiglumis) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na+ concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na+ in leaf of wild species might be affected by OsHKT1;4-mediated Na+ exclusion in leaf and the following Na+ sequestration in leaf might be occurring independent of tonoplast-localized OsNHX1. The newly isolated wild rice accessions will be valuable materials for both rice improvement to salinity stress and the study of salt tolerance mechanism in plants.

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“…The Oryza genus in the grass family ( Poaceae ) contains the cultivated rice species Oryza sativa from Asia and Oryza glabberima from Africa. In addition, the Oryza genus consists of at least 20 wild species with a global distribution which contain an enormous reservoir of untapped variation 1 , 2 . The genus contains mostly diploid (2 n = 24) species with occasional tetraploids (4 n = 48) and can be divided into genome types based on their ability for interbreeding.…”

Section: Introductionmentioning

confidence: 99%

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

et al. 2018

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The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.

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SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza

Cited by 29 publications

References 49 publications

OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

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SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza

Cited by 29 publications

References 49 publications

OsSYL2AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

OsSYL2AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

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OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)