The Wild Relative of Rice: Genomes and Genomics

Sanchez, Paul L.; Wing, Rod A.; Brar, D. S.

doi:10.1007/978-1-4614-7903-1_2

Cited by 114 publications

(99 citation statements)

References 53 publications

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“…Koefisien jarak genetik antarplasma nutfah unggul berdasarkan delapan belas marka SSR dengan metode Nei dan Takezaki (1983 Pemilihan tetua persilangan yang memiliki jarak genetik yang jauh memungkinkan munculnya transgresive segregation pada progeni/keturunan yang dihasilkan. Transgresive segregation adalah pola segregasi dengan keturunan yang dihasilkan memiliki sifat unggul melebihi dua tetuanya (Sanchez et al, 2014). Progeni persilangan generasi awal (F 2 -F 4 ) yang memiliki pola transgresif disebut segregan transgresif.…”

Section: Analisis Kekerabatanunclassified

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Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

Susanto¹,

Satoto²

2018

J. AgroBiogen

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The level of phylogeny among local rice that has identified the resistances to plant pests and diseases needs to be studied to determine the genetic distance, so that information can be used for a recommendation parental crosses. Simple sequence repeat (SSR) markers could be used as one tool to know the degree of phylogeny and the genetic distance between genotypes. The aim of this study was to determine phylogenetic tree and the coefficient of genetic distance of several local rice resistant to host and pest based polymorphic analysis of SSR markers. Fifteen host and pest resistant local rice and one popular variety (Ciherang) were used. Molecular analysis was carried out using eighteen SSR markers. The banding patterns of DNA amplification resulted from PCR on polyacrylamide electrophoresis gel was documented by using UV Transilluminator. The phylogenetic tree showed three clearly separated clusters. Cluster 1 consisted of indica accessions resistant to blast and BLB: Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, and Siawak. Cluster 2 consisted of javanica and indica accessions resistant to BPH, tungro, blast, and BLB: Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, and Jadul. Cluster 3 consisted of japonica accession resistant to blast: Kapas. The farthest genetic distance was between Pare Pulu and Ampek Panjang (DA = 0.816). The closest genetic distance was between Pare Pulu dan Pare Lottong (DA = 0.098). This research data can be used as a reference in determining the crossing parents that will be used in plant breeding program for varieties improvement of Indonesian local rice.Keywords: Genetic distance, local rice, kinship, SSR markers. ABSTRAKTingkat kekerabatan antarpadi lokal dengan keunggulan tahan terhadap hama dan penyakit tanaman (HPT) perlu dipelajari untuk mengetahui seberapa jauh kekerabatannya, sehingga informasi yang diperoleh dapat digunakan untuk kebutuhan pemilihan tetua persilangan. Marka simple sequence repeat (SSR) dapat dijadikan salah satu alat bantu untuk mengetahui tingkat kekerabatan antargenotipe. Penelitian ini bertujuan mengetahui tingkat kekerabatan dan jarak genetik beberapa aksesi padi lokal unggul tahan HPT berdasarkan analisis polimorfisme marka SSR. Materi genetik yang digunakan adalah lima belas padi lokal tahan HPT dan varietas Ciherang. Analisis molekuler dilakukan menggunakan delapan belas marka SSR. Pola pita DNA hasil amplifikasi PCR pada elektroforesis gel poliakrilamida didokumentasi dengan visualisasi gel doc/UV transilluminator. Pohon kekerabatan menunjukkan tiga klaster yang terpisah jelas. Klaster 1 terdiri atas aksesi-aksesi subspesies indica tahan blas dan HDB, yaitu Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, dan Siawak. Klaster 2 terdiri atas aksesi-aksesi subspesies javanica dan japonica tahan WBC, tungro, blas, dan HDB, yaitu Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, dan Jadul. Klaster 3 berisi aksesi subsp...

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Section: Analisis Kekerabatanunclassified

“…Beberapa varietas hasil perakitan yang mendasarkan pemilihan tetua persilangannya berdasarkan jarak genetik yang jauh memiliki sifat unggul, seperti potensi hasil yang tinggi, sifat tahan terhadap penyakit, dan sifat lainnya yang lebih baik dibanding dengan tetuanya. Seperti contohnya yang disampaikan Sanchez et al (2014) …”

Section: Analisis Kekerabatanunclassified

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

Susanto¹,

Satoto²

2018

J. AgroBiogen

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“…Among these sciences are genomics-assisted breeding, other OMICs approaches or systems biology tools for improving crop resiliency for adverse growing environments owing to climate change (Kole et al, 2015, Rabara et al, 2014b, Tripathi et al, 2012. These tools increase the exploitability of rice genetic resources like wild rice species of which desirable traits have been incorporated in modern rice varieties through molecular approaches and tissue culture (Sanchez et al, 2013). To date, advanced techniques can detect the presence of genes or traits expressing tolerance to DS and HTS conditions and measure the efficiency of their use in breeding populations, thus serving as alternative tools for precise breeding of crops that are resilient to adverse growing environments.…”

Section: Advances In Developing Climate-resilient Ricementioning

confidence: 99%

“…Rice germplasms including landraces and traditional varieties serve as sources of genetic materials essential to develop new rice cultivars through advanced rice breeding techniques (Rabara et al, 2014a). In particular, wild rice species have many useful genes for resistance to major biotic and biotic stresses (Sanchez et al, 2013). Their existence endures owing to farmers who continually cultivated and nurtured thousands of rice varieties for several years thereby contributing to rice diversity (Bellon et al, 2000).…”

Section: Phenotyping and Genotyping Of Rice Genetic Resourcesmentioning

confidence: 99%

“…Advances in genomics, molecular marker technology, fluorescence in situ hybridization and tissue culture opened avenues in utilizing the genetic diversity of rice through interspecific hybridization (Sanchez et al, 2013). For example, wild hybridization aided in the development of two Arizona rice varieties with heat tolerance (Sanchez et al, 2013).…”

Section: Mapping Of Genetic Loci (Qtl) and Genome-wide Association Stmentioning

confidence: 99%

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When water runs dry and temperature heats up: Understanding the mechanisms in rice tolerance to drought and high temperature stress conditions

Rabara¹,

Msanne²,

Ferrer³

et al. 2018

Preprint

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Rice production, owing to its high-water requirement for cultivation, is very vulnerable to the threat of changing climate, particularly prolonged drought and high temperature. Such threats heighten the need for abiotic stress-resilient rice varieties with better yield potential. This review examines the physiological and molecular mechanisms of rice varieties to cope with stress conditions of drought (DS), high temperature (HTS) and their combination (DS-HTS). It appraises research studies in rice about its various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for rice varieties with improved resilience to abiotic stresses. This review consolidates available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to climate-induced abiotic stresses. The development of new breeding and cultivation strategies for climate-resilient rice varieties is a challenging task. It requires a comprehensive understanding of the various morphological, biochemical, physiological, and molecular components governing yield under drought and high temperature, but possible by implementing cohesive approaches involving molecular and systems biology approaches in genomics and molecular breeding, including genetic engineering.

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Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA−ARS rice collection

et al. 2020

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Genebanks conserve worldwide crop genetic diversity in systematically assembled and maintained ex situ collections for use by plant breeders and geneticists to improve the productivity, value, and sustainability of agriculture. Challenges faced in genebank management include providing sufficient and accurate trait information to facilitate searching the collection; controlling redundant accessions, seed mixtures, and mislabeled accessions; and identifying gaps in diversity. To help address these issues, a system that employs genotyping using 24 trait‐specific markers (TSMs), fingerprint markers (FPMs), or markers that are unique to subspecies was implemented for the USDA–ARS National Plant Germplasm System (NPGS), National Small Grains Collection (NSGC) for rice (Oryza sativa L.). Trait‐specific markers were used to validate phenotypic data for fragrance, pericarp color, apparent amylose content, starch pasting properties, gelatinization temperature, resistance to rice blast disease, plant pubescence, and plant height. Discrepancies between genotypic and phenotypic data are useful for quality control during curation or may present opportunities for identifying novel alleles, particularly for TSMs. Over 2,000 accessions were classified by species, O. sativa or O. glaberrima Steud.; subspecies, Indica or Japonica; and subpopulation, aromatic, indica, aus, temperate japonica, or tropical japonica using the subspecies marker and FPMs. This small panel of TSMs and FPMs was also adequate for differentiating important U.S. cultivars, which are primarily of tropical japonica background. As a result of this study, TSM and FPM descriptors will be added to the rice NSGC database, redundancies reduced, and mislabeled accessions corrected, thus increasing the value of the rice NSGC for breeding programs and providing new opportunities for gene discovery.

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The Wild Relative of Rice: Genomes and Genomics

Cited by 114 publications

References 53 publications

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

<strong>When water runs dry and temperature heats up: </strong><strong>Understanding the mechanisms in rice tolerance to drought and </strong><strong>high temperature stress conditions</strong>

Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA−ARS rice collection

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