Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Kadapi, Muhamad; Ebana, Kaworu; Fukuoka, Shuichi; Okuno, Kazutoshi

doi:10.1007/s10722-016-0392-1

Cited by 6 publications

(7 citation statements)

References 37 publications

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“…However, the F ST value between the two indica subgroups was very low (0.0721). The average F ST value between the two indica subgroups and the japonica subgroup was 0.489, which indicates that the indica population could be definitively distinguished from the japonica population; this value was similar to the F ST value (0.517) of indica and japonica subspecies as determined via SNP markers (Muhamad et al 2017). The genetic diversity and PIC of our population were 0.28 and 0.24, respectively.…”

Section: Discussionsupporting

confidence: 71%

Development of a core SNP arrays based on the KASP method for molecular breeding of rice

Yang

Chen

et al. 2019

Rice

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Background The development and utilization of genetic markers play a pivotal role in marker-assisted breeding of rice cultivars during pyramiding of valuable genes. Among molecular markers, SNPs have become the most promising due to their wide distribution within genomes and suitability for high -throughput automated genotyping. Although metadata of SNPs have been identified via next generation sequencing in rice, a large gap between the development of SNP markers and the application in breeding still exists. To promote the application of SNP markers based on the KASP (Kompetitive Allele-Specific PCR) method in rice breeding, a set of core SNP arrays was built via the screening of SNP databases and literature resources based on the KASP method. Results Five hundred and ninety six SNPs classified into eight subsets including quality control, indica-indica variation, highly polymorphic, functional genes, key genes targeting sites, gene cloned region, important trait associated and gap filling sites were chosen to design KASP primers and 565 out of them were successfully designed, and the assay design success rate was 94.8%. Finally, 467 out of the 565 successfully-designed SNPs can display diversity at the loci were used to develop a set of core SNP arrays. To evaluate the application value of the core SNP markers in rice breeding, 481 rice germplasms were genotyped with three functional KASP markers designed from the sequences of GBSSI , SSIIa , and Badh2 from the core SNP arrays for estimation of their grain quality performance. Eighteen rice lines, including Xiangwanxian 13, Basmati 370, Ruanhua A, and PR 33319–9–1-1-5-3-5-4-1, harbor all three favorable alleles. The core KASP arrays were also used for rice germplasm assessment, genetic diversity and population evaluation. Four hundred and eighty-one rice germplasms were divided into 3 groups: POP1, POP2 and POP3. POP1 and POP2 were indica rice subgroups consisting of 263 and 186 rice germplasms, respectively. POP3 was a japonica rice subgroup consisting of 32 rice germplasms. The average F ST value for the three subgroups was 0.3501; the F ST value of POP1 and POP3 was the largest (0.5482), while that of POP1 and POP2 was the smallest (0.0721). The results showed that the genetic distance between the japonica and indica rice subspecies was large, indicating that the core SNP markers were effective at discriminating the population structure of the germplasms. Finally, the core KASP arrays were used for association analysis with milled grain traits. A total of 31 KASP markers were significantly associated ( P < 0.01) with ML and the LWR. Among the 31 markers, 13 were developed based on cloned genes or on identified loci related to yield traits. Notably, several KASP markers associated with grain quality were also found...

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Section: Discussionsupporting

confidence: 71%

Development of a core SNP arrays based on the KASP method for molecular breeding of rice

Yang

Chen

et al. 2019

Rice

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“…This variety is from the cross IR18349-53-1-3-1-3/IR19661-131-3-1//IR19661-131-3-1/IR64/IR64, and has high genetic similarity with IR64 (IRRI 2015 ; Septiningsih et al 2014 ). It has very similar grain quality to IR64 and is also morphologically and genetically similar (Muhamad et al 2017 ).…”

Section: Reviewmentioning

confidence: 99%

IR64: a high-quality and high-yielding mega variety

Mackill

Khush

2018

Rice

165

105

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High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.

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“…6). The dendogram could be used in crops differentiation of adaptive traits such in rice (Muhamad et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Chlorophyll Fluorescence and Stomatal Conductance of Ten Sugarcane Varieties under Waterlogging and Fluctuation Light Intensity

Soleh

Ariyanti²,

Dewi³

et al. 2018

Emir J Food Agric

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Under natural conditions, plants are often subjected to waterlogging due to poor soil drainage and or exessive rainfall. This condition leads to reduced maximum quantum yield of photosystem II (fv/fm) under suboptimal growing system. Under well-watered conditions (WW), the fv/fm of ten varieties of sugarcane were maintained at more than 0.78. However, following waterlogging for 4 days and a constant light of 3000 mmolmol-1 for 60s, the fv/fm of ten varieties of sugarcene varied from 0.587 in PS882 (V4) to 0.740 in GMP2 (V9). Meanwhile, under fluctuating light intensity from dark to highlight of 1600 mmolmol-1, the fv/fm of all varieties decreased to below of 0.1 except in the genotype PSJK922 (V5) at 28 DAT (day after treatment) of waterlogging. This difference was then further examined through measurements of stomatal conductance (gs) among the varieties. There was negative correllation between fv/fm and stomatal conductance, high gs was not associated with lower fv/fm. Dendrogam analyses showed the variety of PS881 (V1), PS864 (V3) and Kidang Kencana (KK) were highly sensitive to waterlogging. These results suggest potential screening of plants based on improve fv/fm under abiotic condition.

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Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Cited by 6 publications

References 37 publications

Development of a core SNP arrays based on the KASP method for molecular breeding of rice

Development of a core SNP arrays based on the KASP method for molecular breeding of rice

IR64: a high-quality and high-yielding mega variety

Chlorophyll Fluorescence and Stomatal Conductance of Ten Sugarcane Varieties under Waterlogging and Fluctuation Light Intensity

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