<p>Rice lines for increasing grain yield derived from Code variety that have loci associated to the spikelet number and early heading date (qTSN4 and qDTH8 locus, respectively) have been developed. The objectives of this research were to molecularly analyze, to evaluate the yield of Code-qTSN4 and Code-qDTH8 lines in the field, and to obtain the lines with yield potential of at least 10% higher than that shown by Code. The study was conducted in October 2016 to March 2017. The study was divided into two activities: molecular verification of the qTSN4, qDTH8, and Xa7 loci using specific markers and field trials at two locations in West Java, i.e. Sukamandi Experimental Station and Cianjur farmer’s paddy field. The genetic materials used were 56 rice genotypes consisted of 49 lines (Code-qTSN4 and Code-qDTH8) and 7 check varieties. Molecular analysis showed that all rice lines tested contained qTSN4, qDTH8, and Xa7 loci. All of the loci were in homozygous stage indicating that they were pure lines. Field trial results showed that Cianjur location gave much better on yield component variables than that in Sukamandi. The highest increase in spikelet number was shown by B6-4 planted at Cianjur with increase of 30.06% and B12-2 planted at Sukamandi with increase of 25.15% compared to Code. Both lines were classified as Code-qTSN4 line group. The qTSN4 and qDTH8 loci proved to increase yield more than 20% compared to Code. A total of 34 lines resulted from this study can be used for advanced yield trials conducted at several agro-ecologically different locations.</p>

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...

<p>The challenges in upland rice cultivation are phosphorous (P) deficiency and aluminum (Al) toxicity, each controlled by Pup1 and Alt loci, respectively. Pyramiding the two genes into Indonesian rice varieties were previously done through Marker-Assisted Backcrossing method to obtain BC3F2 populations. The aims of this study were to analyze the BC3F2 upland rice lines containing the Alt and Pup1 loci molecularly (foreground and background analyses) and to test their phenotypic performances. Genetic materials tested included Dupa variety (donor of Alt) and three improved Indonesian genotypes (Dodokan-Pup1, Situ Bagendit-Pup1, and Batur-Pup1) as recurrent parents, Kasalath (donor of Pup1), and 300 BC3F2 lines from Dodokan-Pup1+Alt, Situ Bagendit-Pup1+Alt, and Batur-Pup1+Alt, respectively. The rice genotypes were selected individually using modified Yoshida nutrient solution, followed by foreground and background analyses. 150 out of 300 seedlings were selected and maintained until harvest in the greenhouse. Foreground analysis using markers (RM1361, RM12031, and Kas46-2) and tiller number performances resulted in 18 plants from BC3F2 Dodokan-Pup1+Alt, 30 plants from BC3F2 Situ Bagendit-Pup1+Alt, and 25 plants from BC3F2 Batur-Pup1+Alt still carrying Alt and Pup1 loci. Background analysis using molecular markers showed that the best individual lines of BC3F2 were number 56 for BC3F2 Dodokan-Pup1+Alt, number 32 or 70 for BC3F2 Situ Bagendit-Pup1+Alt, and number 20 for BC3F2 Batur-Pup1+Alt. The selected lines having both both Alt and Pup1 loci in homozygote condition with highest number of tiller per plant which are useful genetic materials for developing upland rice variety tolerance to low P and Al toxicity.</p>