Characterization and Selection of Phosphorus Deficiency Tolerant Rice Genotypes in Sri Lanka

Aluwihare, Y.C.; Ishan, M.; Chamikara, M. D. M.; Weebadde, Cholani; Sirisena, D. N.; Samarasinghe, W. L. G.; Ranaweera, L. T.

doi:10.1016/j.rsci.2015.10.001

Cited by 39 publications

(56 citation statements)

References 32 publications

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“…Aluwihare et al (2016) selected low P tolerant rice genotypes by growing plants in pots filled with soil, collected from cultivated field without P fertilizer application for past 40 years.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, abundant use of P fertilizers derived from livestock manures, a common practice in intensive agriculture, affects environment in the form of eutrophication of freshwater habitats (Tiessen, 2008;Ashley et al, 2011). One approach suggested to tackle this problem of low or excess use of P in farming is the identification and development of genotypes with high phosphorous use efficiency (PUE) in low P soils without compromising yield (Aluwihare et al, 2016;Rose et al, 2010Rose et al, , 2011Rose et al, , 2012Rose et al, , 2015. More than PUE, it is the ability to tolerate P deficiency to different extent and yet give high yield which is more important.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

Yugandhar¹,

Basava²,

Subrahmanyam³

et al. 2017

Aust J Crop Sci

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Mutants are powerful genetic resources in plant breeding and functional genomics studies. Sixty seven stable ethyl methane sulphonate (EMS) induced rice mutants and the wild type parent Nagina 22 (N22) were characterized for plant height, tiller number, panicle number and grain yield under normal, low P field and alternate wet and dry (AWD) conditions in the same season. They were also genotyped with 44 SSR markers and four Pup1 (Phosphorus uptake1) gene specific markers. Genetic diversity was analysed by combining phenotype and marker data using Ward-MLM method. Single marker analysis showed significant association of four markers RM19696, RM263, RM3688 and RM1942 with grain yield in all three conditions. K-1, a Pup1 gene specific marker was significantly associated with tiller number only under low P conditions. The average dissimilarity between mutants was 0.86 and cophenetic correlation coefficient was 0.74. Six mutants were selected as gain-of-function mutants as they showed significantly higher grain yield in all three conditions, compared with N22. The selected mutants are an important resource for gene discovery for enhanced tolerance to low P and water stress conditions and associated markers can be useful in marker assisted selection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

Yugandhar¹,

Basava²,

Subrahmanyam³

et al. 2017

Aust J Crop Sci

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“…The male and female parents and the order of crosses were taken under pedigree history. The average yield of the rice plants, the maturity period in different growing seasons ( Yala and Maha seasons of Sri Lanka [29]), plant height, basal leaf sheath color and additional color patterns, recommended type of the land, level of phosphorus deficiency tolerance, amount of brown rice recovery, milling recovery, head rice recovery, amylose content, gelatinization temperature, weight of 1000 grains, shape of the grain, pericarp color, weight of a kg, color of the buff coat and resistance/susceptibility to pests and diseases; brown planthopper (BPH), bacterial leaf blight and rice blast disease were recorded under phenotypic data (S1 Table). The available DNA marker alleles, marker positions in the linkage map, and allelic scores were entered under molecular data [30–33] (S2 Table).…”

Section: Methodsmentioning

confidence: 99%

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake

Sahibdeen

Udawela³

et al. 2020

Preprint

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17The development of rice cultivars with desirable traits is essential. The decision-making is a 18 crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions 19 if an organized pedigree visualization platform is available for the material of the rice breeding 20 germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved 21 varieties with high yield and other promising traits. In the present study, the available data of 22 all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the 23 related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. 24 Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by 25 Descent (IBD) probabilities were calculated using FlexQTL software and included in the 26 Pedimap database. The parentage selection based on the variations of phenotypic traits, 27 selection of marker alleles for molecular breeding, and detection of the founders of genetic 28 effects can be swiftly conducted using Pedimap. However, the power of harnessing the value 29of Pedimap for making breeding decisions relies on the availability of data for the traits, 30 markers, and genomic sequences. Thus, it is imperative to characterize the breeding 31 germplasms using standard phenomic and genomic characterization procedures before 32 organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each 33 other to produce improved varieties to meet global challenges. 34 35

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“…Tanaman padi dengan rambut akar yang banyak dan panjang, serta cabang perakaran yang banyak sangat bermanfaat untuk menjerap P lebih banyak (Vinod dan Heuer, 2012). Seleksi padi yang toleran defisiensi P telah banyak dilakukan, baik menggunakan larutan hara maupun tanah (Aluwihare et al, 2016;. Namun, seleksi plasma nutfah dalam jumlah ribuan di rumah kaca atau di lapang biasanya memerlukan lahan yang luas (Hadianto et al, 2015;Silitonga dan Risliawati, 2013).…”

Section: Pendahuluanunclassified

Eksplorasi Lokus Pup1 Berbasis Marka Molekuler pada 55 Genotipe Padi

Tasliah

Ma'sumah²,

Prasetiyono³

2018

J. AgroBiogen

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ABSTRACT Phosphorus (P) is an essential nutrient for rice growth. The scarcity of rock phosphate, the main source of P fertilizer, has prompted breeders to seek rice genotypes tolerant to P deficiency by exploring Pup1 locus, which plays a role in the P uptake, among the rice genotypes. This study was aimed at exploring Pup1 locus among 55 rice genotypes to identify genotypes possesing Kasalath alleles at four specific markers of genes in the Pup1 locus and high similarity of nucleotide sequence of the markers compared to Pup1 locus reference sequence. Amplification of genomic DNA of three check genotypes, i.e. Kasalath, NIL-C443, and Nipponbare; 36 upland, 15 lowland, and 1 amphibian rice, with K05−1, K20−2 + Bsp12861, K29−1, and K46−2 markers, showed that the number of upland rice containing Pup1 locus was comparable to lowland rice (49% and 47.3%, respectively). Three genotypes, i.e. Gajah Mungkur, Cabacu, and IR36, contained Kasalath alleles on the four markers, indicating that they have Pup1 locus. Kasalath, NIL-C443, Gajah Mungkur, Cabacu, and IR36 had varying levels of nucleotide sequence similarity based on K20−2 + Bsp12681 and K46−2 marker regions, ranged from 54.7−95.2% and 94.6−97.5%, respectively, compared to the Pup1 reference sequence. Based on Kasalath allelic pattterns and high nucleotide sequence similarity to the Pup1 reference sequence (87.3−92.4% and 94.6−96%, respectively), Gajah Mungkur, Cabacu, and IR35 were identified as new sources of Pup1 locus to replace Kasalath.Keywords: Rice, P deficiency, Pup1, germplasm, sequence analysis. ABSTRAKFosfor (P) merupakan unsur penting pada padi yang ketersediaannya di bumi semakin berkurang. Eksplorasi lokus yang berperan dalam penangkapan P (Pup1) pada plasma nutfah padi bermanfaat untuk mendapatkan calon tetua yang toleran terhadap defisiensi P. Penelitian ini bertujuan mengeksplorasi lokus Pup1 pada 55 genotipe padi guna mendapatkan genotipe yang memiliki alel Kasalath dari empat marka spesifik gen-gen di dalam lokus Pup1 dan memiliki kesamaan sekuen yang tinggi dengan sekuen rujukan lokus Pup1. Hasil amplifikasi DNA genomik dari tiga genotipe padi cek, yaitu Kasalath, NIL-C443, dan Nipponbare; 36 padi gogo, 15 padi sawah, dan 1 padi amfibi, menggunakan empat marka spesifik yang berada di dalam lokus Pup1, yaitu K05−1, K20−2 + Bsp12861, K29−1, dan K46−2, menunjukkan bahwa persentase padi gogo yang memiliki lokus Pup1 hampir sama dengan padi sawah, berturut-turut 49% dan 47,3%. Tiga genotipe, yaitu Gajah Mungkur, Cabacu, dan IR36, memiliki alel Kasalath pada keempat marka yang menunjukkan bahwa genotipe tersebut memiliki lokus Pup1. Kasalath, NIL-C443, Gajah Mungkur, Cabacu, dan IR36 memiliki kesamaan sekuen basa yang bervariasi pada daerah marka K20−2 + Bsp12681 dan K46−2, berturut-turut 54,7−95,2% dan 94,6−97,5%, dibanding dengan sekuen rujukan Pup1. Gajah Mungkur, Cabacu, dan IR36 pada daerah tersebut memiliki kesamaan sekuen basa yang tinggi dibanding dengan sekuen rujukan Pup1 (berturut-turut 87,3−92,4% dan 94,6−96%) sehingga ketiga genotipe m...

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Characterization and Selection of Phosphorus Deficiency Tolerant Rice Genotypes in Sri Lanka

Cited by 39 publications

References 32 publications

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Eksplorasi Lokus Pup1 Berbasis Marka Molekuler pada 55 Genotipe Padi

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