Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Ni, Jinfu; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

doi:10.1038/ncomms6087

Cited by 472 publications

(428 citation statements)

References 39 publications

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“…Begum et al [36] identified seven, 10 and 11 QTL for GW, GL and GLWR, respectively, using advanced lines from IRRI's irrigated breeding program genotyped with 71,710 SNP generated by Genotyping-by-sequencing (GBS). Similarly, using 533 O. sativa landrace and elite accessions genotyped with 4,358,600 SNP derived from GBS, Yang et al [37] identified 10, 11, 19 and 21 QTL for GLWR, TGW, GW and GL, respectively. These studies clearly demonstrated that GWAS offers higher resolution for QTL mapping and can be used as a powerful complementary strategy to the classical linkage mapping using bi-parental segregation populations.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Fang¹,

Yingguo²,

Wu³

et al. 2018

Acta Agronomica Sinica

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Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.

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Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Fang¹,

Yingguo²,

Wu³

et al. 2018

Acta Agronomica Sinica

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“…High-throughput noninvasive phenotyping also has been adopted successfully to assess the genetics of estimated biomass dynamics in maize (Junker et al, 2015;Muraya et al, 2017). In a previous work, a rice automatic phenotyping platform (RAP) was designed to achieve high-throughput screening of rice (Oryza sativa) plants for genetic studies (Yang et al, 2014). In this study, the RAP was expanded for high-throughput phenotyping of maize plants.…”

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confidence: 99%

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth

et al. 2017

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With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

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“…Genotying 199 individu F1 populasi persilangan interspesifik E guineesis x E. Oleifera dapat diselesaikan hanya dalam waktu tiga bulan dan menghasilkan peta genetik dengan kandungan marka molekuler yang padat dibanding peta genetik kelapa sawit sebelumnya berdasarkan marka AFLP dan SSR (Barcelos et al, 2002;Singh et al, 2009;Billotte et al, 2010;Ting et al, 2013). SNP chip tersebut memfasilitasi percepatan pelabelan gen-gen unggul dan aplikasinya pada pemuliaan yang pada akhirnya mempersingkat siklus pemuliaan tanaman kelapa sawit (Yang et al, 2014 …”

Section: Kemajuan Dan Potensi Aplikasiunclassified

PEMANFAATAN TEKNOLOGI GENOMIKA DAN TRANSFORMASI GENETIK UNTUK MENINGKATKAN PRODUKTIVITAS KELAPA SAWIT / The Use of Genomic and Genetic Transformation Technologies for Oil Palm Productivity Improvement

Tasma¹

2017

PSP

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ABSTRAKSalah satu kendala budidaya kelapa sawit adalah rendahnya produktivitas dengan rataan nasional 4 ton minyak/ha/tahun jauh dari potensinya yang dapat mencapai 18,5 ton minyak/ha/tahun. Pemuliaan kelapa sawit secara konvensional sangat lambat dan perlu waktu panjang. Diperlukan 10-12 tahun hanya untuk menyelesaikan satu siklus pemuliaan. Aplikasi teknologi genomika melalui pemuliaan berbantuan marka dan rekayasa genetika mempercepat siklus pemuliaan, mengurangi luas lahan untuk uji daya hasil, dan mempercepat pelepasan varietas unggul kelapa sawit. Tujuan dari tulisan ini untuk mengulas pemanfaatan teknologi genomika dan transformasi genetik untuk perbaikan produktivitas kelapa sawit dan potensi aplikasinya untuk perbaikan produktivitas kelapa sawit di Indonesia. Teknologi genomika telah menghasilkan peta genom acuan dua spesies kelapa sawit (Elaeis guineensis dan Elaeis oleifera) yang menghasilkan gen Shell (Sh) yang mengendalikan heterosis hasil minyak, ditemukan mekanisme terbentuknya buah mantel, dan sebagai fondasi untuk penemuan gen-gen unggul dan pengembangan marka molekuler kapasitas tinggi yang mengakselerasi program pemuliaan kelapa sawit. Pemanfaatan marka gen Sh dan kit pendeteksi bibit penghasil buah mantel mempercepat siklus pemuliaan kelapa sawit dan sarana seleksi bibit tenera unggul untuk menjamin peningkatan produktivitas kelapa sawit. Perbanyakan individu tanaman unggul terpilih dengan teknik kultur in vitro menjamin penggunaan bibit yang seragam di lapang.Teknologi rekayasa genetika potensial digunakan untuk perbaikan bahan tanaman kelapa sawit dengan kualitas dan gizi minyak tinggi serta produk kelapa sawit yang dapat digunakan sebagai bioplastik. Resekuensing tiga genotipe kelapa sawit Indonesia menghasilkan jutaan variasi genom sebagai sumberdaya pemuliaan bernilai tinggi untuk percepatan program pemuliaan kelapa sawit nasional. Teknologi genomika dan rekayasa genetika sangat potensial diaplikasikan di Indonesia mendukung program perbaikan produktivitas dan mutu minyak kelapa sawit nasional.

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Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

Cited by 472 publications

References 39 publications

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth

PEMANFAATAN TEKNOLOGI GENOMIKA DAN TRANSFORMASI GENETIK UNTUK MENINGKATKAN PRODUKTIVITAS KELAPA SAWIT / The Use of Genomic and Genetic Transformation Technologies for Oil Palm Productivity Improvement

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