Journal of Genetics and Genomics

New and Emerging Genomics-based Approaches in Crop Breeding

Bin Han

2012, 39(7): 301-302. doi: 10.1016/j.jgg.2012.06.003

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Tomato Genome Gets Fully Decoded — Paves Way to Tastier and Healthier Fruits

Jianfeng Ren, Changbao Li, Chuanyou Li

2012, 39(7): 303-305. doi: 10.1016/j.jgg.2012.06.001

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Epigenomic Modification and Epigenetic Regulation in Rice

Yu Zhao, Dao-Xiu Zhou

2012, 39(7): 307-315. doi: 10.1016/j.jgg.2012.02.009

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Abstract:
Epigenomes including genome-wide histone modification and DNA methylation profiles are important for genome activity and for defining gene expression patterns of plant development and responses to various environmental conditions. Rice is the most important crop plant and serves as a model for cereal genomics. Rice epigenomic landscape is emerging and the function of chromatin modification regulators in gene expression, transposon repression and plant development is being characterized. Epigenomic variation that gives rise to stable or transgenerational heritable epialleles related to variation of important agronomical traits or stress responses is being characterized in rice. Implication of epigenomic variation in rice heterosis is being exploited.

Recent Developments of Genomic Research in Soybean

Ching Chan, Xinpeng Qi, Man-Wah Li, Fuk-Ling Wong, Hon-Ming Lam

2012, 39(7): 317-324. doi: 10.1016/j.jgg.2012.02.002

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Abstract:
Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data.

Dissecting the Genetic Basis of Extremely Large Grain Shape in Rice Cultivar ‘JZ1560’

Jie-Zheng Ying, Ji-Ping Gao, Jun-Xiang Shan, Mei-Zhen Zhu, Min Shi, Hong-Xuan Lin

2012, 39(7): 325-333. doi: 10.1016/j.jgg.2012.03.001

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Abstract:
Rice grain shape, grain length (GL), width (GW), thickness (GT) and length-to-width ratio (LWR), are usually controlled by multiple quantitative trait locus (QTL). To elucidate the genetic basis of extremely large grain shape, QTL analysis was performed using an F₂ population derived from a cross between a japonica cultivar ‘JZ1560’ (extremely large grain) and a contrastingindica cultivar ‘FAZ1’ (small grain). A total number of 24 QTLs were detected on seven different chromosomes. QTLs for GL, GW, GT and LWR explained 11.6%, 95.62%, 91.5% and 89.9% of total phenotypic variation, respectively. Many QTLs pleiotropically controlled different grain traits, contributing complex traits correlation. GW2 and qSW5/GW5, which have been cloned previously to control GW, showed similar chromosomal locations with qGW2-1/qGT2-1/qLWR2-2 and qGW5-2/qLWR5-1 and should be the right candidate genes. Plants pyramiding GW2 and qSW5/GW5 showed a significant increase in GW compared with those carrying one of the two major QTLs. Furthermore, no significant QTL interaction was observed between GW2 and qSW5/GW5. These results suggested that GW2 and qSW5/GW5 might work in independent pathways to regulate grain traits. ‘JZ1560’ alleles underlying all QTLs contributed an increase in GW and GT and the accumulation of additive effects generates the extremely large grain shape in ‘JZ1560’.

A Pyramid Breeding of Eight Grain-yield Related Quantitative Trait Loci Based on Marker-assistant and Phenotype Selection in Rice (Oryza sativa L.)

Guo Zong, Ahong Wang, Lu Wang, Guohua Liang, Minghong Gu, Tao Sang, Bin Han

2012, 39(7): 335-350. doi: 10.1016/j.jgg.2012.06.004

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Abstract:
1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.

Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G. raimondii Genome

Qin Li, Xiang Jin, Yu-Xian Zhu

2012, 39(7): 351-360. doi: 10.1016/j.jgg.2012.04.008

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Abstract:
The plant genome possesses a large number of microRNAs (miRNAs) mainly 21–24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ∼10million non-coding RNAs (ncRNAs) derived from fiber tissue of the allotetraploid cotton (Gossypium hirsutum) 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D₅ genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10–20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.

Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

Chi Song, Juan Guo, Wei Sun, Ying Wang

2012, 39(7): 361-368. doi: 10.1016/j.jgg.2012.06.002

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Whole genome duplication (WGD) events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods: synonymous substitution rates (Ks) and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes constructed. It was evident that chromosome 2 had experienced an intra-chromosomal duplication event. Major inter-chromosomal duplication occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36–82 million years ago (MYA) and 148–205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosid-asterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis (monocot-dicot).

2012 Vol. 39, No. 7