1.
Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods.
Liu, S, Zhong, H, Meng, X, Sun, T, Li, Y, Pinson, SRM, Chang, SKC, Peng, Z
BMC plant biology. 2020;(1):441
Abstract
BACKGROUND Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. RESULTS To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. CONCLUSIONS While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.
2.
Genetic dissection of QTLs and differentiation analysis of alleles for heading date genes in rice.
Zhang, H, Liu, S, Chen, G, Liu, X, Xuan, N, Yang, Y, Liu, W, Ding, H, Yao, F
PloS one. 2018;(1):e0190491
Abstract
Heading date is an important agronomic trait in rice (Oryza sativa L.); it determines the geographical and seasonal adaptability of the crop. Single segment substitution lines (SSSLs) have become the preferred experimental materials in mapping functional genetic variations as the particular chromosome segments from donor genotypes can be evaluated for their impact on the phenotype in a recurrent recipient background. The phenotypic differences can be attributed to the control of quantitative trait loci (QTLs). Here, we evaluated a library consisting of 1,123 SSSLs in the same genetic background of an elite rice variety, Huajingxian74 (HJX74), and revealed four SSSLs, W05-1-11-2-7-6 (W05), W08-16-3-2 (W08), W12-28-58-03-19-1 (W12), and W22-9-5-2-4-9-3 (W22), which had a significantly different heading date compared to HJX74. To further genetically dissect the QTLs controlling heading date on chromosomes 3, 6, and 10, four SSSLs were used to develop 15 secondary SSSLs with the smaller substituted segments. The qHD-3 heading date QTL detected in W05 and W08 was delimited to an interval of 4.15 cM, whereas qHD-6-1 and qHD-6-2 heading date QTLs dissected from the substituted segments in W12 were mapped to the intervals of 2.25-cM and 2.55-cM, respectively. The qHD-10 QTL detected on the substituted segment in W22 was mapped to an interval of 6.85-cM. The nucleotide and amino acid sequence changes for those genes in the secondary SSSLs were also revealed. The allele variations of those genes might contribute to the heading date QTLs on chromosome 3 (DTH3, OsDof12, and EHD4), chromosome 6 (Hd3a, Hd17, and RFT1), and chromosome 10 (Ehd1 and Ehd2). These sequence variations in heading date genes would be useful resources for further studying the function of genes, and would be important for rice breeding. Overall, our results indicate that secondary SSSLs were powerful tools for genetic dissection of QTLs and identification of differentiation in the genes.
3.
Study of rice pollen grains by multispectral imaging microscopy.
Hu, Y, Wu, Q, Liu, S, Wei, L, Chen, X, Yan, Z, Yu, J, Zeng, L, Ding, Y
Microscopy research and technique. 2005;(6):335-46
Abstract
Cellular images obtained by light microscopy have been analyzed qualitatively, but there is still a lack of quantitative information about the variations in cellular metabolism of selective substances. A new approach using the multispectral imaging microscope (MIM) to observe rice (Oryza sativa L.) pollen grains is reported. A liquid crystal tunable filter device was used for wavelength selection from 400 to 720 nm and a cooled two-dimensional monochrome charge coupled device for image detection. Rice pollen were stained respectively by acetocarmine, Coomassie blue, or iodine potassium-iodine, and then imaged by MIM. The images were processed by the WuDa Image Analysis System 2003 (computer software), and the transmittance spectra for pollen grain images were obtained. The statistical analysis of the transmittance data showed that the macromolecular amount (nucleic acid, protein, starch) of male-sterile line (MSL) pollen grains was less than those of the fertility-maintaining line (FML). For instance there was a significantly lower nucleic acid content in the MSL than in the FML pollen. The results revealed that pollen abortion was directly related to the diminution of intracellular substances for metabolism. Consequently, we have established a quantitative criterion to determine pollen sterility. Comparing the spectra features of the FML with the MSL, we found that certain spectra features can be used to identify various types of abortion pollens and the deficient cytoplasm of male-sterile rice. Our experimental results offer the first quantitative understanding for evaluating cell morphological structure correlated with cellular physiological status.