The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype 3 environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

A doubled haploid (DH) barley (Hordeum vulgare L.) population of 334 lines (ND24260 × Flagship) genotyped with DArT markers was used to map genes for adult plant resistance (APR) to leaf rust (Puccinia hordei Otth) under field conditions in Australia and Uruguay. The Australian barley cultivar Flagship carries an APR gene (qRphFlag) derived from the cultivar Vada. Association analysis and composite interval mapping identified two genes conferring APR in this DH population. qRphFlag was mapped to the short arm of chromosome 5H (5HS), accounting for 64-85% of the phenotypic variation across four field environments and 56% under controlled environmental conditions (CEC). A second quantitative trait locus (QTL) from ND24260 (qRphND) with smaller effect was mapped to chromosome 6HL. In the absence of qRphFlag, qRphND conferred only a low level of resistance. DH lines displaying the highest level of APR carried both genes. Sequence information for the critical DArT marker bPb-0837 (positioned at 21.2 cM on chromosome 5HS) was used to develop bPb-0837-PCR, a simple PCR-based marker for qRphFlag. The 245 bp fragment for bPb-0837-PCR was detected in a range of barley cultivars known to possess APR, which was consistent with previous tests of allelism, demonstrating that the qRphFlag resistant allele is common in leaf rust resistant cultivars derived from Vada and Emir. qRphFlag has been designated Rph20, the first gene conferring APR to P. hordei to be characterised in barley. The PCR marker will likely be effective in marker-assisted selection for Rph20.

A genomic selection index (GSI) is a linear combination of genomic estimated breeding values that uses genomic markers to predict the net genetic merit and select parents from a nonphenotyped testing population. Some authors have proposed a GSI; however, they have not used simulated or real data to validate the GSI theory and have not explained how to estimate the GSI selection response and the GSI expected genetic gain per selection cycle for the unobserved traits after the first selection cycle to obtain information about the genetic gains in each subsequent selection cycle. In this paper, we develop the theory of a GSI and apply it to two simulated and four real data sets with four traits. Also, we numerically compare its efficiency with that of the phenotypic selection index (PSI) by using the ratio of the GSI response over the PSI response, and the PSI and GSI expected genetic gain per selection cycle for observed and unobserved traits, respectively. In addition, we used the Technow inequality to compare GSI vs. PSI efficiency. Results from the simulated data were confirmed by the real data, indicating that GSI was more efficient than PSI per unit of time.

ObjectiveTo determine recent trends in maternal prepregnancy body mass index (BMI) and to quantify its association with birth and maternal outcomes.MethodsA population-based retrospective cohort study included resident women with singleton births in the California Birth Statistical Master Files (BSMF) database from 2007 to 2016. There were 4,621,082 women included out of 5,054,968 women registered in the database. 433,886 (8.6%) women were excluded due to invalid or missing information for BMI. Exposures were underweight (BMI < 18.5 kg/m2), normal weight (18.5–24.9 kg/m2), overweight (25.0–29.9 kg/m2), and obese (≥ 30 kg/m2) at the onset of pregnancy. Obesity was subcategorized into class I (30.0–34.9 kg/m2), class II (35.0–39.9 kg/m2), and class III (≥ 40 kg/m2), while adverse outcomes examined were low birth weight (LBW), very low birth weight (VLBW), macrosomic births, preterm birth (PTB), very preterm birth (VPTB), small-for-gestational-age birth (SGA), large-for-gestational-age birth (LGA), and cesarean delivery (CD). Descriptive analysis, simple linear regression, and multivariate logistic regression were performed, and adjusted odds ratios (AORs) with 95% confidence intervals (CIs) for associations were estimated.ResultsOver the ten-year study period, the prevalence of underweight and normal weight women at time of birth declined by 10.6% and 9.7%, respectively, while the prevalence of overweight and obese increased by 4.3% and 22.9%, respectively. VLBW increased significantly with increasing BMI, by 24% in overweight women and by 76% in women with class III obesity from 2007 to 2016. Women with class III obesity also had a significant increase in macrosomic birth (170%) and were more likely to deliver PTB (33%), VPTB (66%), LGA (231%), and CD (208%) than women with a normal BMI. However, obese women were less likely to have SGA infants; underweight women were 51% more likely to have SGA infants than women with a normal BMI.ConclusionsIn California from 2007 to 2016, there was a declining trend in women with prepregnancy normal weight, and a rising trend in overweight and obese women, particularly obesity class III. Both extremes of prepregnancy BMI were associated with an increased incidence of adverse neonatal outcomes; however, the worse outcomes were prominent in those women classified as obese.

Genotypes produced from plant breeding programs for annual crops are evaluated in multiyear, multilocation field trials where a large number of genotypes grown in a few locations in the first year are progressively reduced by selection and tested in a greater number of locations in successive years. Provided fixed resources are specified, the efficiencies of testing strategies differing in the number of locations and replications used and in the number of genotypes tested in successive years can be evaluated by three statistics (genetic repeatability, acceptance probability, and potential gain) calculated from five variance components applicable to the field trials. The five variance components required are deployed genetic variance, genotype‐by‐year, genotype‐by‐location, and genotype‐by‐year‐by‐location interaction variances and the residual (error) variance. Strictly, known variance components are required, but the statistics and their standard errors can be calculated using robust estimates of the variance components obtained from a combined analysis over years of a large set of historical data from field trials that are connected by shared genotypes across years, as genotype‐by‐year and genotype‐by‐year‐by‐location variance components are estimable. Single‐year analyses are unsuitable, as no estimate of the interactions with year are available, and such analyses produce biased estimates of genetic variance and genotype‐by‐location interaction variance. These procedures are illustrated using an example from the CIMMYT international wheat breeding program to evaluate 2‐yr testing strategies for CIMMYT's Elite Spring Wheat Yield Trials that has been distributed and evaluated internationally since 1979.

BackgroundLow birth weight (LBW) is a leading risk factor for infant morbidity and mortality in the United States. There are large disparities in the prevalence of LBW by race and ethnicity, especially between African American and White women. Despite extensive research, the practice of clinical and public health, and policies devoted to reducing the number of LBW infants, the prevalence of LBW has remained unacceptably and consistently high. There have been few detailed studies identifying the factors associated with LBW in California, which is home to a highly diverse population. The aim of this study is to investigate recent trends in the prevalence of LBW infants (measured as a percentage) and to identify risk factors and disparities associated with LBW in California.MethodsA retrospective cohort study included data on 5,267,519 births recorded in the California Birth Statistical Master Files for the period 2005–2014. These data included maternal characteristics, health behaviors, information on health insurance, prenatal care use, and parity. Logistic regression models identified significant risk factors associated with LBW. Using gestational age based on obstetric estimates (OA), small for gestational age (SGA), appropriate for gestational age (AGA) and large for gestational age (LGA) infants were identified for the periods 2007–2014.ResultsThe number of LBW infants declined, from 37,603 in 2005 to 33,447 in 2014. However, the prevalence of LBW did not change significantly (6.9% in 2005 to 6.7% in 2014). The mean maternal age at first delivery increased from 25.7 years in 2005 to 27.2 years in 2014. The adjusted odds ratio showed that women aged 40 to 54 years were twice as likely to have an LBW infant as women in the 20 to 24 age group. African American women had a persistent 2.4-fold greater prevalence of having an LBW infant compared with white women. Maternal age was a significant risk factor for LBW regardless of maternal race and ethnicity or education level. During the period 2017–2014, 5.4% of the singleton births at 23–41 weeks based on OE of gestational age were SGA infants (preterm SGA + term SGA). While all the preterm SGA infants were LBW, both preterm AGA and term SGA infants had a higher prevalence of LBW.ConclusionsIn California, during the 10 years from 2005 to 2014, there was no significant decline in the prevalence of LBW. However, maternal age was a significant risk factor for LBW regardless of maternal race and ethnicity or education level. Therefore, there may be opportunities to reduce the prevalence of LBW by reducing disparities and improving birth outcomes for women of advanced maternal age.Electronic supplementary materialThe online version of this article (10.1186/s40748-018-0084-2) contains supplementary material, which is available to authorized users.

BackgroundPreterm birth (PTB) is associated with increased infant mortality, and neurodevelopmental abnormalities among survivors. The aim of this study is to investigate temporal trends, patterns, and predictors of PTB in California from 2007 to 2016, based on the obstetric estimate of gestational age (OA).MethodsA retrospective cohort study evaluated 435,280 PTBs from the 5,137,376 resident live births (8.5%) documented in the California Birth Statistical Master Files (BSMF) from 2007 to 2016. The outcome variable was PTB; the explanatory variables were birth year, maternal characteristics and health behaviors. Descriptive statistics and logistic regression analysis were used to identify subgroups with significant risk factors associated with PTB. Small for gestational age (SGA), appropriate for gestational age (AGA) and large for gestational age (LGA) infants were identified employing gestational age based on obstetric estimates and further classified by term and preterm births, resulting in six categories of intrauterine growth.ResultsThe prevalence of PTB in California decreased from 9.0% in 2007 to 8.2% in 2014, but increased during the last 2 years, 8.4% in 2015 and 8.5% in 2016. Maternal age, education level, race and ethnicity, smoking during pregnancy, and parity were significant risk factors associated with PTB. The adjusted odds ratio (AOR) showed that women in the oldest age group (40–54 years) were almost twice as likely to experience PTB as women in the 20- to 24-year reference age group. The prevalence of PTB was 64% higher in African American women than in Caucasian women. Hispanic women showed less disparity in the prevalence of PTB based on education and socioeconomic level. The analysis of interactions between maternal characteristics and perinatal health behaviors showed that Asian women have the highest prevalence of PTB in the youngest age group (< 20 years; AOR, 1.40; 95% confidence interval (CI), 1.28–1.54). Pacific Islander, American Indian, and African American women ≥40 years of age had a greater than two-fold increase in the prevalence of PTB compared with women in the 20–24 year age group. Compared to women in the Northern and Sierra regions, women in the San Joaquin Valley were 18%, and women in the Inland Empire and San Diego regions 13% more likely to have a PTB. Women who smoked during both the first and second trimesters were 57% more likely to have a PTB than women who did not smoke. Compared to women of normal prepregnancy weight, underweight women and women in obese class III were 23 and 33% more likely to experience PTB respectively.ConclusionsImplementation of public health initiatives focusing on reducing the prevalence of PTB should focus on women of advanced maternal age and address race, ethnic, and geographic disparities. The significance of modifiable maternal perinatal health behaviors that contribute to PTB, e.g. smoking during pregnancy and prepregnancy obesity, need to be emphasized during prenatal care.Electronic supplementary materialThe online version of this ar...

Objective To identify current maternal and infant predictors of infant mortality, including maternal sociodemographic and economic status, maternal perinatal smoking and obesity, mode of delivery, and infant birthweight and gestational age. Methods This retrospective study analyzed data from the linked birth and infant death files (birth cohort) and live births from the Birth Statistical Master files (BSMF) in California compiled by the California Department of Public Health for 2007-2015. The birth cohort study comprised 4,503,197 singleton births including 19,301 infant deaths during the nine-year study period. A subpopulation to study fetal growth consisted of 4,448,300 birth cohort records including 13,891 infant deaths. Results The infant mortality rate (IMR) for singleton births decreased linearly (p <0.001) from 4.68 in 2007 to 3.90 (per 1,000 live births) in 2015. However, significant disparities in IMR were uncovered in different population groups depending upon maternal sociodemographic and economic characteristics and maternal characteristics during pregnancy. Children of African American women had almost twice the risk of infant mortality when compared with children of White women (AOR 2.12; 95% CI, 1.98-2.27; p<0.001). Infants of women with Bachelor's degrees or higher were 89% less likely to die (AOR 1.89; 95% CI, 1.76-2.04; p<0.001) when compared to infants of women with education less than high school. Infants of maternal smokers were 75% more likely to die (AOR 1.75; 95% CI, 1.58-1.93; p<0.001) than infants of nonsmokers. Infants of women who were overweight and obese during pregnancy accounted for 55% of IMR over all women in the study. More than half of the infant deaths