Genetic Erosion from Modern Varieties into Traditional Upland Rice Cultivars (Oryza sativa L.) in Northern Thailand

Ishikawa, Ryuji; Yamanaka, Shinşuke; Fukuta, Yoshimichi; Chitrakon, Songkran; Bounphanousay, Chay; Kanyavong, K.; Tang, Ling-hua; Nakamura, Ikuo; Satô, Tadashi; Sato, Yoichiro

doi:10.1007/s10722-004-6132-y

Cited by 20 publications

(14 citation statements)

References 22 publications

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“…Suh et al (1997) reported that weedy strains in Korea possessed indica and japonica characteristics in mixture. Such a genetic feature was also found in Bhutan and Northeast Thailand (Ishikawa et al , 2006. In addition, the weedy strains are increasing even where no wild relatives are growing nearby (Ishikawa et al , 2006.…”

Section: Introductionmentioning

confidence: 72%

“…Such a genetic feature was also found in Bhutan and Northeast Thailand (Ishikawa et al , 2006. In addition, the weedy strains are increasing even where no wild relatives are growing nearby (Ishikawa et al , 2006. Some of these weedy strains were heterozygous for codominant nuclear markers such as isozymes which carry indica-or japonica-specific alleles (Ishikawa et al , 2006.…”

Section: Introductionmentioning

confidence: 83%

“…Some of these weedy strains were heterozygous for codominant nuclear markers such as isozymes which carry indica-or japonica-specific alleles (Ishikawa et al , 2006. Cytoplasmic markers also suggested that the weedy strains were generated by indica-japonica crossing because they showed different combinations of plastid and nuclear types (Ishikawa et al 2006).…”

Section: Introductionmentioning

confidence: 99%

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Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan

et al. 2009

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Weedy rice (Oryza sativa L.) plants found in Okayama, Japan, exhibit various morphophysiological characteristics, and are roughly classified into japonica-type and indica-type. We characterized the weedy strains collected from nine sites with molecular markers in flanking regions of two diagnostic isozyme loci, Acp1 and Sdh1. Haplotype analysis for closely-linked SSR markers flanking Acp1 revealed that 1) japonica-type weedy strains shared the same haplotypes with local varieties, and 2) indica-type weedy strains carrying an indica-specific isozyme allele possessed two haplotypes. One of the two haplotypes was common to a forage variety, 'Moretsu'. PCR analysis revealed that the dwarf weedy strains carried the deletion inside OsGA20ox2 as the semi-dwarf allele (sd1). The deletion was also found in 'Moretsu'. The other haplotype was shared with indica forage variety, 'Tetep', which showed the same sequence haplotype for Sdh1 with the indica-type weedy strains. The results obtained from this study suggested that the weedy strains in Okayama have multiple origins and semi-dwarfness possibly derived from 'Moretsu' or indica modern varieties.

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Section: Introductionmentioning

confidence: 72%

Section: Introductionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

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Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan

et al. 2009

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“…However, some authors consider that genetic erosion has taken place as soon as new alleles are introduced through introgression from advanced cultivars into traditional landraces (Ishikawa et al, 2006), as the original genotype will then have changed. However, this ignores the dynamic nature of the management of landraces by farmers.…”

Section: Varietal Erosionmentioning

confidence: 99%

Genetic erosion in crops: concept, research results and challenges

et al. 2009

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The loss of variation in crops due to the modernization of agriculture has been described as genetic erosion. The current paper discusses the different views that exist on the concept of genetic erosion in crops. Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop. Two stages in this bottleneck are recognized: the initial replacement of landraces by modern cultivars; and further trends in diversity as a consequence of modern breeding practices. Genetic erosion may occur at three levels of integration: crop, variety and allele. The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level. According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following: a reduction in diversity due to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed.

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“…These accessions might still share identical by descent segments since derivation from common ancestors. One possible factor contributing to such incongruous ndings that cannot be neglected is introgression owing to gene ow among wild species, landraces, and cultivars (Ishikawa et al 2006. For example, a mega variety TC65 inherited photoperiodinsensitive alleles of Heading date 1 (Hd1) and Early heading date 1 (Ehd1) from two landraces, Muteke and Nakabo, by spontaneous introgression of natural gene ow during modern breeding (Wei et al 2016).…”

Section: The Genetic Diversity and Differentiation In The Collected Rmentioning

confidence: 99%

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Hour

Hsieh

Chang

et al. 2020

Preprint

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Background: Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5,000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement.Results: A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding.Conclusions: The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

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Genetic Erosion from Modern Varieties into Traditional Upland Rice Cultivars (Oryza sativa L.) in Northern Thailand

Cited by 20 publications

References 22 publications

Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan

Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan

Genetic erosion in crops: concept, research results and challenges

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

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