Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

/pdf/genome-wide-association-studies-of-14-agronomic-traits-in-4ds8wectal.pdf

Genome-wide association studies of 14 agronomic traits in rice landraces

http://image.sciencenet.cn/olddata/kexue.com.cn/upload/blog/file/2008/8/20088317044836131.pdf

The Molecular Genetics of Crop Domestication

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

/pdf/a-map-of-rice-genome-variation-reveals-the-origin-of-29qusn0uvd.pdf

A map of rice genome variation reveals the origin of cultivated rice

In this review, recent developments and future prospects of obtaining a better understanding of the regulation of nitrogen use efficiency in the main crop species cultivated in the world are presented. In these crops, an increased knowledge of the regulatory mechanisms controlling plant nitrogen economy is vital for improving nitrogen use efficiency and for reducing excessive input of fertilizers, while maintaining an acceptable yield. Using plants grown under agronomic conditions at low and high nitrogen fertilization regimes, it is now possible to develop whole-plant physiological studies combined with gene, protein, and metabolite profiling to build up a comprehensive picture depicting the different steps of nitrogen uptake, assimilation, and recycling to the final deposition in the seed. A critical overview is provided on how understanding of the physiological and molecular controls of N assimilation under varying environmental conditions in crops has been improved through the use of combined approaches, mainly based on whole-plant physiology, quantitative genetics, and forward and reverse genetics approaches. Current knowledge and prospects for future agronomic development and application for breeding crops adapted to lower fertilizer input are explored, taking into account the world economic and environmental constraints in the next century.

/pdf/the-challenge-of-improving-nitrogen-use-efficiency-in-crop-13ff0obvfv.pdf

The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches

Filamins are large actin-binding proteins that stabilize delicate three-dimensional actin webs and link them to cellular membranes. They integrate cellular architectural and signalling functions and are essential for fetal development and cell locomotion. Here, we describe the history, structure and function of this group of proteins.

Filamins as integrators of cell mechanics and signalling.

The waxy (Wx) gene of rice encodes a granule-bound starch synthase (GBSS = waxy protein) required for the synthesis of amylose in endosperm. An analysis of Wx transcripts, Wx protein, and amylose content of 31 rice cultivars revealed that endosperm amylose and Wx protein contents are correlated with the ability of the cultivar to excise intron I from the leader sequence of the Wx transcript. Cultivars with high endosperm amylose content (group I) contain high levels of amylose, Wx protein, and the mature 2.3 kb Wx mRNA. Cultivars with intermediate amylose content (group II) produce substantial amounts of a large 3.3 kb Wx pre-mRNA, with intron I still present, in addition to the mature Wx mRNA, and intermediate levels of Wx protein. Glutinous rice (group III cultivars) contains no amylose, no Wx protein, and no mature Wx mRNA; only the incompletely spliced 3.3 kb Wx pre-mRNA is present in group III cultivars. Based on these results, it is hypothesized that the amylose content of rice endosperm is regulated at the level of Wx transcript processing, and, more specifically, at the stage of intron I excision from the Wx pre-mRNA.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.1995.7040613.x

The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene.

The unidirectional movements of the microtubule-associated motors, dyneins, and kinesins, provide an important mechanism for the positioning of cellular organelles and molecules. An intriguing possibility is that this mechanism may underlie the directed transport and asymmetric positioning of morphogens that influence the development of multicellular embryos. In this report, we characterize the Drosophila gene, Dhc64C, that encodes a cytoplasmic dynein heavy chain polypeptide. The primary structure of the Drosophila cytoplasmic dynein heavy chain polypeptide has been determined by the isolation and sequence analysis of overlapping cDNA clones. Drosophila cytoplasmic dynein is highly similar in sequence and structure to cytoplasmic dynein isoforms reported for other organisms. The Dhc64C dynein transcript is differentially expressed during development with the highest levels being detected in the ovaries of adult females. Within the developing egg chambers of the ovary, the dynein gene is predominantly transcribed in the nurse cell complex. In contrast, the encoded dynein motor protein displays a striking accumulation in the single cell that will develop as the oocyte. The temporal and spatial pattern of dynein accumulation in the oocyte is remarkably similar to that of several maternal effect gene products that are essential for oocyte differentiation and axis specification. This distribution and its disruption by specific maternal effect mutations lends support to recent models suggesting that microtubule motors participate in the transport of these morphogens from the nurse cell cytoplasm to the oocyte.

/pdf/drosophila-cytoplasmic-dynein-a-microtubule-motor-that-is-5tdsiu0n0y.pdf

Drosophila cytoplasmic dynein, a microtubule motor that is asymmetrically localized in the oocyte.

The microtubule motor cytoplasmic dynein has been implicated in a variety of intracellular transport processes. We previously identified and characterized the Drosophila gene Dhc64C, which encodes a cytoplasmic dynein heavy chain. To investigate the function of the cytoplasmic dynein motor, we initiated a mutational analysis of the Dhc64C dynein gene. A small deletion that removes the chromosomal region containing the heavy chain gene was used to isolate EMS-induced lethal mutations that define at least eight essential genes in the region. Germline transformation with a Dhc64C transgene rescued 16 mutant alleles in the single complementation group that identifies the dynein heavy chain gene. All 16 alleles were hemizygous lethal, which demonstrates that the cytoplasmic dynein heavy chain gene Dhc64C is essential for Drosophila development. Furthermore, our failure to recover somatic clones of cells homozygous for a Dhc64C mutation indicates that cytoplasmic dynein function is required for cell viability in several Drosophila tissues. The intragenic complementation of dynein alleles reveals multiple mutant phenotypes including male and/or female sterility, bristle defects, and defects in eye development.

https://www.genetics.org/content/genetics/142/3/865.full.pdf

Cytoplasmic Dynein Function Is Essential in Drosophila melanogaster

The maize genome has been shown to contain six glutamine synthetase (GS) genes with at least four different expression patterns. Noncoding 3′ gene-specific probes were constructed from all six GS cDNA clones and used to examine transcript levels in selected organs by RNA gel blot hybridization experiments. The transcript of the single putative chloroplastic GS2 gene was found to accumulate primarily in green tissues, whereas the transcripts of the five putative GS1 genes were shown to accumulate preferentially in roots. The specific patterns of transcript accumulation were quite distinct for the five GS1 genes, with the exception of two closely related genes.

Differential expression of six glutamine synthetase genes in Zea mays

The interactions of three subunits of cytoplasmic dynein from Drosophila melanogaster, LC8, Tctex-1, and the N-terminal domain of IC74 (N-IC74, residues 1-289), were characterized in vitro by affinity methods, limited proteolysis, and circular dichroism spectroscopy. These subunits were chosen for study because they are presumed to promote the assembly of the complex and to be engaged in the controlled binding and release of cargo. Limited proteolysis and mass spectrometry of N-IC74 in the presence of LC8 and Tctex-1 localized binding of Tctex-1 to the vicinity of K104 and K105, and localized binding of LC8 to the region downstream of K130. Circular dichroism, fluorescence, sedimentation velocity, and proteolysis studies indicate that N-IC74 has limited secondary and tertiary structure at near physiological solution conditions. Upon addition of LC8, N-IC74 undergoes a significant conformational change from largely unfolded to a more ordered structure. This conformational change is reflected in increased global protection of N-IC74 from proteolytic digestion following the interaction, and in a significant change in the CD signal. A smaller but reproducible change in the CD spectra was observed upon Tctex-1 binding as well. The increased structure introduced into N-IC74 upon light chain binding suggests a mechanism by which LC8 and Tctex-1 may regulate the assembly of the dynein complex.

/pdf/interactions-of-cytoplasmic-dynein-light-chains-tctex-1-and-14guzgvoy6.pdf

Mingang Li

Papers

The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene.

Drosophila cytoplasmic dynein, a microtubule motor that is asymmetrically localized in the oocyte.

Cytoplasmic Dynein Function Is Essential in Drosophila melanogaster

Differential expression of six glutamine synthetase genes in Zea mays

Interactions of cytoplasmic dynein light chains Tctex-1 and LC8 with the intermediate chain IC74.