Hybrid breeding of rice via genomic selection

Hybrid breeding is the main strategy for improving productivity in many crops, especially in rice and maize. Genomic hybrid breeding is a technology that uses whole-genome markers to predict future hybrids. Predicted superior hybrids are then field evaluated and released as new hybrid cultivars after their superior performances are confirmed. This will increase the opportunity of selecting true superior hybrids with minimum costs. Here, we used genomic best linear unbiased prediction to perform hybrid performance prediction using an existing rice population of 1495 hybrids. Replicated 10-fold cross-validations showed that the prediction abilities on ten agronomic traits ranged from 0.35 to 0.92. Using the 1495 rice hybrids as a training sample, we predicted six agronomic traits of 100 hybrids derived from half diallel crosses involving 21 parents that are different from the parents of the hybrids in the training sample. The prediction abilities were relatively high, varying from 0.54 (yield) to 0.92 (grain length). We concluded that the current population of 1495 hybrids can be used to predict hybrids from seemingly unrelated parents. Eventually, we used this training population to predict all potential hybrids of cytoplasm male sterile lines from 3000 rice varieties from the 3K Rice Genome Project. Using a breeding index combining 10 traits, we identified the top and bottom 200 predicted hybrids. SNP genotypes of the training population and parameters estimated from this training population are available for general uses and further validation in genomic hybrid prediction of all potential hybrids generated from all varieties of rice.

Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation

BACKGROUND

Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation.

RESULTS

cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together.

CONCLUSIONS

The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.

Factors That Influence Pancreatic Beta Cell Function and Insulin Resistance in Newly Diagnosed Type 2 Diabetes Patients: A Sub-Analysis of the MARCH Trial

INTRODUCTION

The Metformin and Acarbose in Chinese as the initial Hypoglycemic treatment (MARCH) trial has demonstrated a similar efficacy in HbA1c reduction between acarbose and metformin treatments in newly diagnosed type 2 diabetes mellitus (T2DM) patients. The current sub-analysis of the MARCH trail aims to evaluate the baseline characteristics that may influence the improvement of pancreatic β-cell function and insulin resistance after acarbose therapy in Chinese patients with newly diagnosed T2DM.

METHODS

Of the 784 patients who entered the MARCH trail, 391 were assigned to the acarbose therapy group; 304 of these completed 48 weeks of follow-up of acarbose therapy. At 48 weeks, on the basis of the tertiles of change in homeostasis model assessment-beta cell function (∆HOMA-β) and homeostasis model assessment-insulin resistance (∆HOMA-IR), the subjects were divided into lowly, mediumly, and highly improved groups.

RESULTS

In the highly improved HOMA-β group, patients had higher systolic blood pressure (SBP), 2-h postprandial blood glucose (PBG), hemoglobin A1c (HbA1c), and lower high-density lipoprotein cholesterol (HDL-c), fasting serum insulin (FINS) concentration, and HOMA-IR in comparison to the lowly improved group (p < 0.05). A positive correlation was observed between HbA1c, SBP, and highly improved ∆HOMA-β (p < 0.05), while an inverse correlation was evident between HDL-c and highly improved ∆HOMA-β (p < 0.05). The highly improved HOMA-IR group had a significantly higher body mass index (BMI), fasting blood glucose (FBG), FINS concentration, and HOMA-β in comparison to the lowly improved group (p < 0.05). A positive correlation was observed between FBG, waist circumference, and highly improved HOMA-IR (p < 0.05).

CONCLUSION

Newly diagnosed T2DM Chinese patients with lower baseline HDL-c and higher HbA1c and SBP values are more likely to achieve improvement in beta cell function whereas baseline fasting blood glucose and waist circumference were the significant factors associated with improvement in insulin resistance with acarbose therapy.

TRIAL REGISTRATION

The clinical trial registry number was ChiCTR-TRC-08000231.