Frequency Of Favorable Alleles Research Articles

Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry.

Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pathogen, began surfacing in California, Florida, and elsewhere. This disease has since become one of the most common causes of plant death and yield losses in strawberry. The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses. Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious. The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress. The genetic gains were immediate and dramatic. The frequency of highly resistant individuals increased from 1% in selection cycle 0 to 74% in selection cycle 2. Using GWAS and survival analysis, we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance. An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies, which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.

Multilocus functional characterization of indigenous and exotic inbreds for dgat1-2, fatb, ge2 and wri1a genes affecting kernel oil and fatty acid profile in maize

Demand for maize oil is progressively increasing due to its diverse industrial applications, aside from its primary role in human nutrition and animal feed. Oil content and composition are two crucial determinants of maize oil in the international market. As kernel oil in maize is a complex quantitative trait, improving this trait presents a challenge for plant breeders and biotechnologists. Here, we characterized a set of 292 diverse maize inbreds of both indigenous and exotic origin by exploiting functional polymorphism of the dgat1-2, fatb, ge2, and wri1a genes governing kernel oil in maize. Genotyping using gene-based functional markers revealed a lower frequencies of dgat1-2 (0.15) and fatb (0.12) mutant alleles and a higher frequencies of wild-type alleles (Dgat1-2: 0.85; fatB: 0.88). The favorable wri1a allele was conserved across genotypes, while its wild-type allele (WRI1a) was not detected. In contrast, none of the genotypes possessed the ge2 favorable allele. The frequency of favorable alleles of both dgat1-2 and fatb decreased to 0.03 when considered together. Furthermore, pairwise protein-protein interactions among target gene products were conducted to understand the effect of one protein on another and their responses to kernel oil through functional enrichments. Thus, the identified maize genotypes with dgat1-2, fatb, and wri1a favourable alleles, along with insights gained through the protein-protein association network, serve as prominent and unique genetic resources for high-oil maize breeding programs. This is the first comprehensive report on the functional characterization of diverse genotypes at the molecular and protein levels.

Realized genetic gains via recurrent selection in a tropical maize haploid inducer population and optimizing simultaneous selection for the next cycles

AbstractPlant breeders widely use recurrent selection schemes to increase the frequency of favorable alleles for quantitative traits in a population. Although simultaneous selection is complex because it involves several traits combined with selection cycles, the use of selection indexes (SI) is applied to increase the chance of success of the breeding program. Despite many indices are available in the literature, simulations can help breeders to determine which selection index can be better adjusted considering the selection goals, the intensity, and the genetic correlation among traits over breeding cycles. In this context, we estimated the realized genetic gains in a tropical maize haploid inducer population after two cycles of recurrent selection, using external testers and optimizing the simultaneous selection for this breeding population in the long term via stochastic simulations. Furthermore, we proposed a new approach to optimize the initial weights by applying Smith‐Hazel method to maximize the genetic gains for all traits in a balanced way. Overall, the estimated gains in real induction rate were about 63% per cycle, improving the population performance from 0.8% to 2.8%. Moreover, our results confirm that the traditional Smith‐Hazel approach outperformed other methods for long‐term response to selection. Finally, recurrent selection with external testers may be a suitable method to improve the haploid induction rate in tropical maize populations.

Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population.

Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and/or performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic variability in a set of doubled haploid (DH) lines derived from the unselected Iowa Stiff Stalk Synthetic (BSSS) maize population, denoted as C0 (BSSS(R)C0), the seventeenth cycle of reciprocal recurrent selection in BSSS (BSSS(R)C17), denoted as C17 and the cross between BSSS(R)C0 and BSSS(R)C17 denoted as C0/C17. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Additionally, we quantify the contribution of the BSSS progenitors in each set of DH lines. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. Which was observed by the degree of differentiation between the C0_DHL versus C17_DHL groups by Wright's F-statistics (FST). Similarly for the population structure based on principal component analysis (PCA) revealed a clear separation among groups of DH lines. Some of the progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable allele frequencies in the BSSS maize population through the reciprocal recurrent selection program.

Population improvement via recurrent selection drives genetic gain in upland rice breeding.

One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha-1 per cycle or 67.8 kg.ha-1 per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1128 kg.ha-1. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.

Genomic Prediction of Resistance to Tan Spot, Spot Blotch and Septoria Nodorum Blotch in Synthetic Hexaploid Wheat

Genomic prediction combines molecular and phenotypic data in a training population to predict the breeding values of individuals that have only been genotyped. The use of genomic information in breeding programs helps to increase the frequency of favorable alleles in the populations of interest. This study evaluated the performance of BLUP (Best Linear Unbiased Prediction) in predicting resistance to tan spot, spot blotch and Septoria nodorum blotch in synthetic hexaploid wheat. BLUP was implemented in single-trait and multi-trait models with three variations: (1) the pedigree relationship matrix (A-BLUP), (2) the genomic relationship matrix (G-BLUP), and (3) a combination of the two matrices (A+G BLUP). In all three diseases, the A-BLUP model had a lower performance, and the G-BLUP and A+G BLUP were statistically similar (p ≥ 0.05). The prediction accuracy with the single trait was statistically similar (p ≥ 0.05) to the multi-trait accuracy, possibly due to the low correlation of severity between the diseases.

Conservatively transmitted alleles of key agronomic genes provide insights into the genetic basis of founder parents in bread wheat (Triticum aestivum L.)

BackgroundFounder parents play extremely important roles in wheat breeding. Studies into the genetic basis of founder parents and the transmission rules of favorable alleles are of great significance in improving agronomically important traits in wheat.ResultsHere, a total of 366 founder parents, widely grown cultivars, and derivatives of four representative founder parents were genotyped based on efficient kompetitive allele-specific PCR (KASP) markers in 87 agronomically important genes controlling yield, quality, adaptability, and stress resistance. Genetic composition analysis of founder parents and widely grown cultivars showed a consistently high frequency of favorable alleles for yield-related genes. This analysis further showed that other alleles favorable for resistance, strong gluten, dwarf size, and early heading date were also subject to selective pressure over time. By comparing the transmission of alleles from four representative founder parents to their derivatives during different breeding periods, it was found that the genetic composition of the representative founder parents was optimized as breeding progressed over time, with the number and types of favorable alleles carried gradually increasing and becoming enriched. There are still a large number of favorable alleles in wheat founder parents that have not been fully utilized in breeding selection. Eighty-seven agronomically important genes were used to construct an enrichment map that shows favorable alleles of four founder parents, providing an important theoretical foundation for future identification of candidate wheat founder parents.ConclusionsThese results reveal the genetic basis of founder parents and allele transmission for 87 agronomically important genes and shed light on breeding strategies for the next generation of elite founder parents in wheat.

Selection of common bean parents and segregating populations targeting fusarium wilt resistance and grain yield

The present work aimed to select populations for the breeding of common bean targeting fusarium wilt resistance and grain yield. Twelve carioca bean lines, which mainly differ in fusarium wilt resistance and grain yield, were crossed in a 6x6 partial diallel scheme. The parents and their 36 F1’s hybrids were evaluated for fusarium wilt severity caused by FOP isolate UFV 01 (FWS), and grain yield (YIELD). 34 F4’s populations, 12 parents and three other lines were also evaluated for grain yield per plant. The data of F1's parents and hybrids were submitted to diallel analysis. Using the grain yield data per plant, the potential of the 34 F4’s populations was predicted by the Jinks and Pooni method (1976). In the diallel analysis, BRSMG Talismã, CVIII 8511, BRS Pérola, VC 25 and VC 13 stood out in terms of the frequency of favorable alleles for FWS. Except for BRSMG Uai and IAC Formoso, these lines presented the most dominant genes associated in Fusarium wilt resistance. For YIELD, there was a predominance of dominant genes determining higher yield. The 20 F4’s populations with the highest potential included the best 12 of the 20 populations, based on diallel analysis for YIELD. Thus, the 12 populations received the addition of four that were highlighted only by the methodology of Jinks and Pooni (1976), and four based on diallel analysis, which totaled 20 populations. The use of information from more advanced inbreeding generations in complementarity with those of diallel is a promising strategy.

Selecting tropical wheat genotypes through combining ability analysis.

The selection of parents to originate promising base populations, as well as the knowledge of the gene effects controlling agronomic traits by means of diallel, are useful to drive genetic gains in Brazilian tropical wheat breeding programs. The goals of this study were to select tropical wheat parents with a high frequency of favorable alleles and segregating populations with high potential to originate superior progenies through partial diallel analysis. Thus, 14 parents were divided in two groups and crossed in a 7 × 7 partial diallel scheme to originate 49 F1 combinations. After obtaining F2 generation, the populations and the parents were evaluated in the field in the summer of 2021. Days for heading, plant height, rust and yellow spot resistance, and grain yield were evaluated. The data were subjected to partial diallel analysis. There were significant effects of general combining ability for all traits. The specific combining ability effect was significant for days for heading and plant height. The additive gene effects were predominant over the non-additive ones. The parents with the highest frequency of favorable alleles for the traits evaluated were selected in each group. Four populations with high genetic potential to originate superior progenies were selected.

Multi-trait selection of wheat lines under drought-stress condition

The immediate need for the increase in wheat production to meet the future world demand, associated with the occurrence of drastic climatic events, such as drought, makes it necessary to develop drought-resilient genotypes. The aims of this work were to evaluate the use of drought-tolerance indices for the selection of wheat genotypes, to compare the genetic gains in grain yield using different selection strategies by means of a multi-trait index, and to select superior drought-tolerant wheat genotypes. The total of 31 tropical wheat lines was evaluated in two experiments. Five agronomic traits were accessed. The grain yield data from the stress and nonstress experiments were used to obtain five drought-tolerance indices. The data were subjected to mixed model analysis, and four selection scenarios were designed. There was a significant effect of genotype for all traits. The inclusion of drought-tolerance indices in the selection index provided superior genetic gains in drought condition. Seven lines were selected due the high frequency of favorable alleles for drought-tolerance and other important agronomic traits. Drought-tolerance indices are appropriate for characterizing the response of wheat genotypes to drought-stress. The inclusion of drought-tolerance indices along with agronomic traits in multi-trait selection strategies provides for superior gains in grain yield compared to the non-inclusion of the indices.

Genetic analysis using Griffing’s approach for forage yield and components in sorghum

The present study was carried out using seven parental lines including check CSV 46F and their 21 diallel crosses, excluding reciprocal. The experiment was evaluated in randomised block design with three replications during Kharif 2021 at the Centre for Millets Research, Sardarkrushinagar Dantiwada Agricultural University, Deesa. The analysis of variance (mean sum of squares) revealed significant differences for the genotypes, parents, hybrids and parents vs. hybrids among most of the characters, which explained a sufficient amount of heterosis and was reflected in crosses for fodder yield and its attributing characters. The parents SH 1488 and DS 200 recorded maximum mean performance for green forage yield and dry fodder yield per plant. The result of ANOVA for combining ability revealed that the mean sum of squares due to GCA and SCA were found highly significant for studied characters. The ratio ( 2GCA/ 2SCA) of variances for various characters bare standing of non-additive gene action type in the appearance of forage yield and supporting characters. The parent CSV 21F was found to be a good general combiner for green fodder yield per plant. While, parents SH 1488, DS 200 and CSV 21F were found to be good general combiners for dry fodder yield. The parent SSG 59-3 was a very good general combiner for days to flowering, total plant height, stem diameter, crude protein and HCN content. The crosses S 652 × CSV 46F, DS 200 × CSV 21F and SSG 59-3 × S 652 for green fodder yield per plant, while SSG 59-3 × S 652, DS 200 × CSV 21F and SSG 59-3 × CSV 46F for dry fodder yield per plant recorded the highest sca effects. Based on all the genetic parameters, the crosses SSG 59-3 × S 652, SH 1488 × S 652, SH 1488 × DSF 182 and DS 200 × CSV 21F with high mean performance, high sca effects and at least one parent having good to moderate gca effects would increase the frequency of favourable alleles. Therefore, it may be hopeful to select good homozygous lines to ameliorate respective characters in forage sorghum. It can also be used directly in varietal breeding programmes. Keywords: Forage sorghum, Heterosis, GCA, SCA and forage yield.

Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F1 Populations (Lowland x Coastal and Coastal x Upland).

The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from “Alamo”) and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from “Summer”) with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.

Genetic Trends in Fusarium Head Blight Resistance from 20 Years of Winter Wheat Breeding and Cooperative Testing in the Northern U.S.A.

Fusarium head blight (FHB) is a devastating disease of wheat and barley. In the U.S.A., a significant long-term investment in breeding FHB-resistant cultivars began after the 1990s. However, to this date, no study has been performed to understand and monitor the rate of genetic progress in FHB resistance as a result of this investment. Using 20 years of data (1998 to 2018) from the Northern Uniform and Preliminarily Northern Uniform winter wheat scab nurseries that consisted of 1,068 genotypes originating from nine different institutions, we studied the genetic trends in FHB resistance within the northern soft red winter wheat growing region using mixed model analyses. For the FHB resistance traits incidence, severity, Fusarium-damaged kernels, and deoxynivalenol content, the rate of genetic gain in disease resistance was estimated to be 0.30 ± 0.1, 0.60 ± 0.09, and 0.37 ± 0.11 points per year, and 0.11 ± 0.05 parts per million per year, respectively. Among the five FHB-resistance quantitative trait loci assayed for test entries from 2012 to 2018, the frequencies of favorable alleles from Fhb 2DL Wuhan1 W14, Fhb Ernie 3Bc, and Fhb 5A Ning7840 were close to zero across the years. The frequency of the favorable at Fhb1 and Fhb 5A Ernie ranged from 0.08 to 0.33 and 0.06 to 0.20, respectively, across years, and there was no trend in changes in allele frequencies over years. Overall, this study showed that substantial genetic progress has been made toward improving resistance to FHB. It is apparent that today's investment in public wheat breeding for FHB resistance is achieving results and will continue to play a vital role in reducing FHB levels in growers' fields.

Selection of Elite dura-Type Parents to Produce Dwarf Progenies of Elaeis guineensis Using Genetic Parameters

The low annual growth rate of the stipe in oil palm progenies is desirable to increase these crops’ productive and economic life. Recurrent reciprocal selection (R.R.S.) has allowed the development of oil palm populations through several breeding cycles with an increased frequency of favorable alleles associated with traits of interest. The present study evaluated families derived from Deli dura × African dura crosses. For 12 years, the yield, vegetative characteristics, and the amount of oil in seven dura progenies were assessed to estimate, from the information collected, the genetic parameters, heritability, and phenotypic correlations among quantitative genetic traits of high-yielding dwarf progenies. The analysis was carried out using analysis of variance, followed by a comparison of means for all estimated traits. The effect of the progenies was highly significant (p ≤ 0.01) for most traits. The yield values, expressed in fresh fruit bunches (FFB) for the progenies, ranged from 165 to 208 kg per palm per year. The oil-to-bunch ratio (O/B) ranged from 17% to 19%, with an overall average of 18%. One of the essential characteristics in this study was the vertical growth of the stipe. Progenies P6 and P7 were identified as those with the lowest annual increase in height, with values of 0.29 and 0.33 m year−1. The values indicate that these are slow-growing cultivars with a high FFB yield and O/B. The highest heritabilities were found for the vegetative trait height (71.62%) and the number of leaflets (46.64%). The development of dura parents with slow growth characteristics in combination with a high bunch and oil production allows extending the productive life of the crop to more than 35 years, providing added value to obtaining differentiated cultivars of oil palm.

PHENOTYPIC AND GENETIC PARAMETERS ESTIMATED FOR FRESH CORN UNDER DIFFERENT NUTRIENT AVAILABILITY1

ABSTRACT The objective of this work was to estimate and compare phenotypic and genetic parameters after three cycles of intrapopulation recurrent selection for fresh corn grown under three nutrient availability conditions. Three experiments derived from the same population (MV-003) were conducted to assess the ability of progenies to absorb nutrients, one under adequate fertilization (control; MV-006), one under low nitrogen availability (N; MV-006N), and one under low phosphorus availability (P; MV-006P). The experiments were carried out in randomized blocks, with 64 half-sib progenies and three replications for each nutritional condition. Chlorophyll index, plant height, ear insertion, ear diameter, ear length, unhusked ear yield, and marketable husked ear were evaluated. The populations showed variability for the three nutrient availability conditions. The variability reduced after only three selection cycles; thus, evaluating a higher number of half-sib progenies, above 64, under low N and P availability is indicated. The rates used to identify the most efficient progenies in breeding programs should be close to the appropriate one, with a slow reduction after the selection cycles. The variability will be thus maintained, with a greater possibility of identifying more promising progenies. In addition, the frequency of favorable alleles increases more gradually and effectively. The N and P rate of 60 kg ha-1 is not indicated as a critical level for the initial phase of the program.

Genomic Selection in Sugarcane: Current Status and Future Prospects.

Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12–14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes.

Marker based enrichment of provitamin A content in two tropical maize synthetics

Most of the maize (Zea mays L.) varieties in developing countries have low content of micronutrients including vitamin A. As a result, people who are largely dependent on cereal-based diets suffer from health challenges due to micronutrient deficiencies. Marker assisted recurrent selection (MARS), which increases the frequency of favorable alleles with advances in selection cycle, could be used to enhance the provitamin A (PVA) content of maize. This study was carried out to determine changes in levels of PVA carotenoids and genetic diversity in two maize synthetics that were subjected to two cycles of MARS. The two populations, known as HGA and HGB, and their advanced selection cycles (C1 and C2) were evaluated at Ibadan in Nigeria. Selection increased the concentrations of β-carotene, PVA and total carotenoids across cycles in HGA, while in HGB only α-carotene increased with advances in selection cycle. β-cryptoxanthine increased at C1 but decreased at C2 in HGB. The levels of β-carotene, PVA, and total carotenoids increased by 40%, 30% and 36% respectively, in HGA after two cycles of selection. α-carotene and β-cryptoxanthine content improved by 20% and 5%, respectively after two cycles of selection in HGB. MARS caused changes in genetic diversity over selection cycles. Number of effective alleles and observed heterozygosity decreased with selection cycles, while expected heterozygosity increased at C1 and decreased at C2 in HGA. In HGB, number of effective alleles, observed and expected heterozygosity increased at C1 and decreased at C2. In both populations, fixation index increased after two cycle of selections. The greatest part of the genetic variability resides within the population accounting for 86% of the total genetic variance. In general, MARS effectively improved PVA carotenoid content. However, genetic diversity in the two synthetics declined after two cycles of selection.

Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass

Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication traits in the fourth cycle IWG breeding population at the University of Minnesota: height, seed length, seed width, shattering, threshability, and seed mass. A weak population structure was observed and linkage disequilibrium (r2) declined rapidly: 0.23 mega base pairs at conventional r2 value of 0.2. Broad-sense heritabilities were overall high and ranged from 0.71–0.92. Association analysis was carried out using 25,909 single SNP markers and 5379 haplotype blocks. Thirty-one SNP markers and 17 haplotype blocks were significantly associated with the domestication traits. These associations were of moderate effect as they explained 4–6% of the observed phenotypic variation. Ten SNP markers were also detected by the haplotype association analysis. One SNP marker on Chromosome 8, also discovered in haplotype block analysis, was common between seed length and seed mass. Increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG’s domestication traits.

Recurrent selection for resistance to Thrips tabaci in a tropical onion population

Recurrent selection for resistance to onion Thrips tabaci has not been well studied by breeding programmes. Onion thrips is a pest of major concern and is controlled by insecticide spraying, raising production costs and potentially damaging the environment. This study aimed to estimate onion bulb yield genetic gain through six cycles in the ‘BRS Alfa São Francisco’ developed by recurrent selection for T. tabaci resistance. Experiments were carried out in a randomised block design, with three replications, in two locations. The degree of infestation in plants was evaluated five times after transplanting, as well as plant architecture traits and bulb yield. The latest selection cycle presented bulb commercial yield of 32.1 t.ha-1, while the base population ‘Alfa Tropical’ and IPA 10 check cultivar 15.9 and 14.0 t.ha-1, respectively (p<0.01). The broad sense heritability values ranged from 0.65 to 0.74 for bulb yield. The mean genetic gain was 1.0 t.ha-1 or 6% per selection cycle, indicating the efficiency of the method to increase the frequency of favourable alleles for thrips resistance and the possibility of onion cultivation in the total absence of insecticide applications to control this pest, or a reduction in their number

QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice.

Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).