Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets

Robust Stereoscopic Crosstalk Prediction

We propose a new metric to predict perceived crosstalk using the original images rather than both the original and ghosted images. The proposed metrics are based on color information. First, we extract a disparity map, a color difference map, and a color contrast map from original image pairs. Then, we use those maps to construct two new metrics (Vdispc and Vdlogc). Metric Vdispc considers the effect of the disparity map and the color difference map, while Vdlogc addresses the influence of the color contrast map. The prediction performance is evaluated using various types of stereoscopic crosstalk images. By incorporating Vdispc and Vdlogc, the new metric Vpdlc is proposed to achieve a higher correlation with the perceived subject crosstalk scores. Experimental results show that the new metrics achieve better performance than previous methods, which indicate that color information is one key factor for crosstalk visible prediction. Furthermore, we construct a new data set to evaluate our new metrics

Complex genetic architecture underlying the plasticity of maize agronomic traits

Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude -related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compen-sation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental vari-ation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by -environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture

Genome-Wide Association Studies Identified Three Independent Polymorphisms Associated with α-Tocopherol Content in Maize Kernels

Tocopherols are a class of four natural compounds that can provide nutrition and function as antioxidant in both plants and animals. Maize kernels have low α-tocopherol content, the compound with the highest vitamin E activity, thus, raising the risk of vitamin E deficiency in human populations relying on maize as their primary vitamin E source. In this study, two insertion/deletions (InDels) within a gene encoding γ-tocopherol methyltransferase, Zea mays VTE4 (ZmVTE4), and a single nucleotide polymorphism (SNP) located ∼85 kb upstream of ZmVTE4 were identified to be significantly associated with α-tocopherol levels in maize kernels by conducting an association study with a panel of ∼500 diverse inbred lines. Linkage analysis in three populations that segregated at either one of these three polymorphisms but not at the other two suggested that the three polymorphisms could affect α-tocopherol content independently. Furthermore, we found that haplotypes of the two InDels could explain ∼33% of α-tocopherol variation in the association panel, suggesting ZmVTE4 is a major gene involved in natural phenotypic variation of α-tocopherol. One of the two InDels is located within the promoter region and associates with ZmVTE4 transcript level. This information can not only help in understanding the underlying mechanism of natural tocopherol variations in maize kernels, but also provide valuable markers for marker-assisted breeding of α-tocopherol content in maize kernels, which will then facilitate the improvement of maize as a better source of daily vitamin E nutrition

Photosynthesis responses of endemic shrubs of Taklimakan Desert to adverse temperature, humidity and radiation

Under the native habitat conditions, the seasonal gas exchange characteristics of two natural endemic plant species, Calligonum taklimakanensis B.R. Pan & GM. Shen and Tamarix taklamakanensis M.T. Liu, which are located in the hinterland of the Taklimakan Desert, are measured and compared by Li-6400 photosynthesis system. The results indicate that temperature (degrees C), solar radiation (PAR), soil water content (SWC), and other environmental factors have obvious seasonal variations and the gas exchange characteristics of two plants have different changes in different growing seasons. For C. taklimakanensis, both in July and September, its daily changes of net photosynthetic rate tend to be obvious double peak curve, but in July its peak appeared earlier. Besides its maximum net photosynthetic rate (P-max), apparent quantum efficiency (Phi), range of effective photosynthetic radiation significantly less than that in September. Moreover, its water use efficiency (WUE) in July was also lower than that in September due to the higher transpiration rate (T-r). For T. taklamakanensis, although its daily change of net photosynthetic rate is a single peak curve in September, its peak time has not changed, and except that its WUE is higher in September like C. taklimakanensis, the maximum net photosynthetic rate (P-max), apparent quantum efficiency (Phi), light saturation point, and range of effective photosynthetic radiation has not changed or slightly declined. That is to say C. taklimakanensis select a season that habitat was better (like September) to progress relative effectively photosynthesis accumulation, in contrast, T. taklamakanensis still keep a relatively stable photosynthesis rate in different growth seasons. The difference of gas exchange characteristics of the two plants in different seasons shows that adaptation strategies of the two plants to extreme conditions in desert are different. Besides, both the higher photosynthetic accumulation rate and the higher water use efficiency in September also indicate that these two endemic desert shrubs possess the abilities and strategies to make the best of limited natural resources

Upregulation of PIP3-dependent Rac exchanger 1 (P-Rex1) promotes prostate cancer metastasis.

Excessive activation of G-protein-coupled receptor (GPCR) and receptor tyrosine kinase (RTK) pathways has been linked to prostate cancer metastasis. Rac activation by guanine nucleotide exchange factors (GEFs) plays an important role in directional cell migration, a critical step of tumor metastasis cascades. We found that the upregulation of P-Rex1, a Rac-selective GEF synergistically activated by Gbetagamma freed during GPCR signaling, and PIP3, generated during either RTK or GPCR signaling, strongly correlates with metastatic phenotypes in both prostate cancer cell lines and human prostate cancer specimens. Silencing endogenous P-Rex1 in metastatic prostate cancer PC-3 cells selectively inhibited Rac activity and reduced cell migration and invasion in response to ligands of both epidermal growth factor receptor and G-protein-coupled CXC chemokine receptor 4. Conversely, expression of recombinant P-Rex1, but not its \u27GEF-dead\u27 mutant, in non-metastatic prostate cancer cells, such as CWR22Rv1, increased cell migration and invasion through Rac-dependent lamellipodia formation. More importantly, using a mouse xenograft model, we showed that the expression of P-Rex1, but not its mutant, induced lymph node metastasis of CWR22Rv1 cells without an effect on primary tumor growth. Thus, by functioning as a coincidence detector of chemotactic signals from both GPCRs and RTKs, P-Rex1-dependent activation of Rac promotes prostate cancer metastasis