Identification of new sources of bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in wild Oryza species and O. glaberrima

Vikal, Yogesh; Das, A. K.; Patra, Bhaskar Chandra; Goel, R. K.; Sidhu, J. S.; Singh, Kuldeep

doi:10.1017/s147926210777661x

Cited by 34 publications

(16 citation statements)

References 12 publications

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“…(African rice) are the two cultivated rice species in Asia and Africa, respectively ( Chang, 1976 ). Several African rice accessions have adaptive or protective mechanisms of resistance/tolerance to major abiotic and biotic stresses, including drought, iron toxicity, weed competitiveness, nematodes, African rice gall midge, and bacterial blight ( Jones et al, 1997b ; Linares, 2002 ; Vikal et al, 2007 ). However, African rice has its own weakness, including lodging, limited number of spikelets per panicle, grain shattering, and prolonged seed dormancy ( Ndjiondjop et al, 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Ndjiondjop

Semagn

Sow³

et al. 2018

Front. Plant Sci.

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Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.

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Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Ndjiondjop

Semagn

Sow³

et al. 2018

Front. Plant Sci.

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“…oryzae (Xoo). Bakteri Xoo ini merupakan patogen terbawa benih pada padi, yang dapat menurunkan mutu benih dan produksi padi hingga 50-60% (Vikal et al, 2007).…”

Section: Pendahuluanunclassified

Peningkatan Mutu Fisiologis dan Daya Simpan Benih serta Ketahanan Patogen dan Agen Hayati pada Benih Padi Berpelapis

et al. 2017

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“…Xoo merupakan penyebab hawar daun bakteri pada tanaman padi dan merupakan salah satu penyakit yang dapat ditularkan melalui patogen terbawa benih (Agarwal and Sinclair 1996). Penyakit ini dapat menurunkan produksi padi sampai 50% (Vikal et al 2007). Sementara itu Xco adalah bakteri terbawa benih penyebab penyakit bacterial leaf streak yang merupakan salah satu penyakit penting dan banyak ditemukan pada tanaman padi (Swing et al 1990).…”

Section: Perkembangan Bakteri Terbawa Benih Padiunclassified

Keefektifan Pelapisan Benih terhadap Peningkatan Mutu Benih Padi Selama Penyimpanan

Ikrarwati¹,

Ilyas²,

Yukti³

2015

j. penelit. pertan. tanam. pangan

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Identification of new sources of bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in wild Oryza species and O. glaberrima

Cited by 34 publications

References 12 publications

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Peningkatan Mutu Fisiologis dan Daya Simpan Benih serta Ketahanan Patogen dan Agen Hayati pada Benih Padi Berpelapis

Keefektifan Pelapisan Benih terhadap Peningkatan Mutu Benih Padi Selama Penyimpanan

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