Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure

Heuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hajime; Matsumoto, Takashi; Leon, Teresa De; Ulat, Victor Jun; Yano, Masahiro; Wissuwa, Matthias

doi:10.1111/j.1467-7652.2009.00415.x

Cited by 89 publications

(84 citation statements)

References 46 publications

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“…In a similar experiment, NILs segregating for the Pup1 locus (+Pup1: NILs 6-4, Y-4, 14-4; −Pup1: NILs 26-6, 28-10, and Nipponbare) were grown for 50 days in either Pdeficient or P-fertilized soil, and root material was sampled and immediately shock-frozen in liquid N. Some genotype information on these NILs can be found in Heuer et al (2009), Torabi et al (2009), and Wissuwa et al (2002. Total RNA was extracted and used to compare the relative expression of XTH and NAD(P)H-dependent oxidoreductase genes through RT-qPCR.…”

Section: Methodsmentioning

confidence: 99%

“…Annotations of candidate genes at the fine-mapped Pup1 locus have not revealed any gene related to mechanisms known to directly affect P uptake or P metabolism (Heuer et al 2009), and only two of the genes present at the Pup1 locus are present on the Agilent 22 k array. It was therefore not the objective of this study to identify Pup1 candidate genes but rather to identify tolerance mechanisms and regulatory patterns affected by the Pup1 locus.…”

Section: Introductionmentioning

confidence: 99%

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Stress Response Versus Stress Tolerance: A Transcriptome Analysis of Two Rice Lines Contrasting in Tolerance to Phosphorus Deficiency

Pariasca‐Tanaka

Satoh

Rose

et al. 2009

Rice

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Transcriptional profiling has identified genes associated with adaptive responses to phosphorus (P) deficiency; however, distinguishing stress response from tolerance has been difficult. We report gene expression patterns in two rice genotypes (Nipponbare and NIL6-4 which carries a major QTL for P deficiency tolerance (Pup1)) grown in soil with/without P fertilizer. We tested the hypotheses that tolerance of NIL6-4 is associated with (1) internal P remobilization/redistribution; (2) enhanced P solubilization and/or acquisition; and (3) root growth modifications that maximize P interception. Genes responding to P supply far exceeded those differing between genotypes. Genes associated with internal P remobilization/ redistribution and soil P solubilization/uptake were stress responsive but often more so in intolerant Nipponbare. However, genes putatively associated with root cell wall loosening and root hair extension (xyloglucan endotransglycosylases/hydrolases and NAD(P)H-dependent oxidoreductase) showed higher expression in roots of tolerant NIL6-4. This was supported by phenotypic data showing higher root biomass and hair length in NIL6-4.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Stress Response Versus Stress Tolerance: A Transcriptome Analysis of Two Rice Lines Contrasting in Tolerance to Phosphorus Deficiency

Pariasca‐Tanaka

Satoh

Rose

et al. 2009

Rice

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“…Near-isogenic lines bearing the Kasalath allele at Pup1 showed 3-fold higher P uptake and grain yield in low-P trials compared with the recurrent parent, cv Nipponbare, which is intolerant to P starvation (Wissuwa and Ae, 2001). Following high-resolution mapping of Pup1, comparative sequence analyses of homologous bacterial artificial chromosomes showed that a Kasalath genomic fragment contained several genes not present in cv Nipponbare, highlighting an approximately 90-kb deletion in the cv Nipponbare reference genome that encompassed the Pup1 locus (Heuer et al, 2009). Within this insertion/deletion, OsPupK46-2, a gene encoding a Ser/Thr kinase of the Receptor-like Protein Kinase LRK10L-2 subfamily, was found to enhance grain yield and P uptake in rice lines overexpressing this gene, indicating that this protein kinase underlies the Pup1 locus (Gamuyao et al, 2012).…”

mentioning

confidence: 99%

“…In rice (Oryza sativa), Phosphorus uptake1 (Pup1), a major quantitative trait locus (QTL) for P deficiency tolerance donated by an aus-type Indian variety, Kasalath, was mapped to the long arm of chromosome 12 (Ni et al, 1998;Wissuwa et al, 1998Wissuwa et al, , 2002Heuer et al, 2009). Near-isogenic lines bearing the Kasalath allele at Pup1 showed 3-fold higher P uptake and grain yield in low-P trials compared with the recurrent parent, cv Nipponbare, which is intolerant to P starvation (Wissuwa and Ae, 2001).…”

mentioning

confidence: 99%

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

et al. 2014

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Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.

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“…Analisis sekuen pada daerah lokus Pup1 untuk membandingkan sekuen Kasalath dengan basis data Nipponbare telah dilakukan dan diketahui terdapat beberapa sekuen Kasalath yang unik yang tidak dimiliki oleh Nipponbare (Heuer et al, 2009). Di dalam lokus tersebut, terdapat beberapa gen penting yang terlibat dalam penangkapan P. Salah satunya adalah gen phosphorus-starvation tolerance (Pstol1).…”

Section: Pendahuluanunclassified

Analisis Molekuler dan Uji Daya Hasil Galur-Galur Pup1

Prasetiyono¹,

Tasliah²,

Hidayatun³

et al. 2018

J. AgroBiogen

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Improved rice varieties at areas that have problems with the availability of phosphorus (P) is very important. Pup1 locus, the locus containing genes that play a role in the P uptake, has been well mapped and some markers for selection have been developed. Based on previous studies, BC 2 F 8 lines have been obtained from crosses of Dodokan × Kasalath (DK), Dodokan × NIL-C443 (DN), Situ Bagendit × Kasalath (SK), Situ Bagendit × NIL-C443 (SN), Batur × Kasalath (BK), and Batur × NIL-C443 (BN). This study aimed to evaluate the BC 2 F 8 lines at molecular level as well as their yield potential. The molecular research was conducted from November 2013 to June 2014 at ICABIOGRAD, Indonesia and IRRI, Philippines, whereas the field trials were conducted at Taman Bogo Field Station, Lampung and a farmer's land at Sukabumi, West Java. Molecular analysis demonstrated that all of the BC 2 F 8 -Pup1 lines contained Pup1 locus. However, three lines (B5-SK5, B9-SN2, and C9-BN2) containing the Pup1 locus were found in heterozygotes condition. All of the Pup1 lines still retained the genome composition of the parent, except for B7-SK7, C10-BN3, and C11-BN4. B1-SK1, B2-SK2, B3-SK3, B4-SK4, B6-SK6, B9-SN2, C4-BK4, C7-BK7, and C12-BN5 Pup1 lines have yield more than their recurrent parents (Situ Bagendit or Batur) in areas with either low or enough available P conditions. B6-SK6 dan C12-BN5 Pup1 lines have yield more than their recurrent parents and check varieties (Inpago 7 dan Inpago 8) in area with low available P condition. These lines could be used for multilocation trial.Keywords: Rice, Pup1, molecular analysis, yield potency. ABSTRAKPerbaikan varietas padi untuk daerah yang memiliki masalah ketersediaan fosfor (P) sangat penting dilakukan. Lokus Pup1 sebagai lokus yang berisi gen-gen yang berperan dalam penangkapan P telah dipetakan dengan baik dan marka untuk seleksinya telah dibuat. Berdasarkan penelitian sebelumnya, telah diperoleh galur BC 2 F 8 persilangan Dodokan × Kasalath (DK), Dodokan × NIL-C443 (DN), Situ Bagendit × Kasalath (SK), Situ Bagendit × NIL-C443 (SN), Batur × Kasalath (BK), dan Batur × NIL-C443 (BN). Penelitian ini bertujuan menganalisis galur-galur BC 2 F 8 secara molekuler dan mengevaluasi potensi hasil galurgalur tersebut pada kondisi lapang yang berbeda. Penelitian berlangsung mulai bulan November 2013 s.d. Juni 2014. Penelitian molekuler dilakukan di BB Biogen, Indonesia dan IRRI, Filipina, sedangkan penelitian lapang dilakukan di KP Taman Bogo, Lampung dan lahan petani di Sukabumi, Jawa Barat. Berdasarkan analisis molekuler, diperoleh hasil seluruh galur BC 2 F 8 mengandung lokus Pup1, namun ada tiga galur (B5-SK5, B9-SN2, dan C9-BN2) yang mengandung lokus Pup1 dalam kondisi heterozigot. Susunan genom sebagian besar galur Pup1 masih mengikuti susunan genom tetuanya, kecuali B7-SK7, C10-BN3, dan C11-BN4. Galur B1-SK1, B2-SK2, B3-SK3, B4-SK4, B6-SK6, B9-SN2, C4-BK4, C7-BK7, dan C12-BN5 memiliki bobot ubinan lebih banyak dibanding dengan tetua pemulihnya (Situ Bagendit atau Batur) pada kondisi ...

show abstract

Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure

Cited by 89 publications

References 46 publications

Stress Response Versus Stress Tolerance: A Transcriptome Analysis of Two Rice Lines Contrasting in Tolerance to Phosphorus Deficiency

Stress Response Versus Stress Tolerance: A Transcriptome Analysis of Two Rice Lines Contrasting in Tolerance to Phosphorus Deficiency

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

Analisis Molekuler dan Uji Daya Hasil Galur-Galur Pup1

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