Marker-assisted Recurrent Selection Research Articles

Genetic dissection of green pod yield in dolichos bean, an orphan vegetable legume, using new molecular markers.

In the era of genomic-assisted breeding for crop improvement, developing new molecular markers and validating them for use in breeding programs are the prelude. Dolichos bean is one of the most important vegetable legume crops owing to its nutrient-rich green pods used as vegetables. Limitations in genomic resources, including molecular markers, restrict the accelerated improvement of the crop. In the present investigation, a set of 430 new simple sequence repeat markers was developed from sequence information of a reference variety. These markers included di- and tri-nucleotide repeats. The markers were assayed on an association panel, which was evaluated for green pod yield over 5years. A multi-locus model, FarmCPU, was used to assess the marker-trait association analysis. A total of 106 marker-trait associations were identified using an efficient mixed-model approach. Tri-nucleotide repeats were more informative and predominantly associated with trait. Among these markers, 17 were associated with a high level of significance. Markers LP-D-68 and LP-D-14 were identified with a high level of significance in 5-year pooled data and explained 12.70% and 12% of the phenotypic variance, respectively. These markers associated with a high level of confidence have significant scope for use in marker-assisted selection programmes. Other associated markers may be utilized for improving parents through marker-assisted recurrent selection or genomic selection programs.

A review on molecular breeding techniques: Crucial approach in livestock improvement

For underdeveloped countries, molecular breeding (MB) has a lot of promise. However, the implementation in developing countries is far from uniform. Livestock improvement programs aim to improve the genetics of domesticated animal populations by selecting males and females who, when mated, will produce progeny that perform better than the current generation's average. The amount of genetic progress made through conventional selection and breeding methods for quantitative traits in livestock is successful, but limitations such as routinely recording phenotypes, animal sacrifice for meat quality traits, recording in particular sex for sex-limited traits, and so on the limit the amount of genetic progress made through conventional selection and breeding methods. Marker-assisted selection (MAS), genome-wide selection (GWS), marker-assisted recurrent selection (MARS), and genome-wide sequencing (GS) are examples of modern breeding procedures. Molecular genetics technology may provide a technique to choose breeding animals at an early age (even embryos), to select for a wide variety of features and to improve the accuracy of forecasting an individual's mature phenotype. This paper examines the challenges and potential of applying molecular breeding techniques to improve livestock in developing countries.

Prospects of Marker-Assisted Recurrent Selection: Current Insights and Future Implications

Prospects of Marker-Assisted Recurrent Selection: Current Insights and Future Implications

Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat.

Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.

Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.

High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133cM across 16 linkage groups and 2169cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

The effects of a few important gene families on sorghum agronomic traits

Sorghum (Sorghum bicolor [L.] Moench), a main food for more than 500 million impoverished and food insecure people in arid and semi-arid regions of Sub-Saharan Africa (SSA) and South Asia, is an important crop for food and nutritional security (SA). Sorghum has the most acceptance in these drought-prone areas due to its good tolerance to harsh settings, high yield, and use as a good source of forages. In this review, the objective of this study is to document the production and use Sorghum in improvement programmed through a literature review, we used publications from journals to explore gene families, how they evolved, gene family theories, how gene families influenced agronomic features in sorghum, and in-depth studies of the key ten gene families in sorghum. The future prospects on sorghum enhancement include genomic selections and gene families, as well as comparative genomic selections. Furthermore, understanding the mechanism of these gene families is important for addressing problems that plague sorghum production, including as infections, drought, and heat stress. We can accurately improve traits using modern techniques such as marker-assisted selection, Genomic selections (GS), Marker-assisted backcrossing (MABC), Marker-assisted recurrent selection (MARS), Marker-assisted selections (MAS), and Genome-wide selections (GWAS) if we have the above gene families of interest (GWAS). Sorghum as a desirable breed: future paths and prospects.

Marker-Assisted Recurrent Selection for Pyramiding Leaf Rust and Coffee Berry Disease Resistance Alleles in Coffea arabica L.

In this study, marker-assisted recurrent selection was evaluated for pyramiding resistance gene alleles against coffee leaf rust (CLR) and coffee berry diseases (CBD) in Coffea arabica. A total of 144 genotypes corresponding to 12 hybrid populations from crosses between eight parent plants with desired morphological and agronomic traits were evaluated. Molecular data were used for cross-certification, diversity study and resistance allele marker-assisted selection (MAS) against the causal agent of coffee leaf rust (Hemileia vastatrix) and coffee berry disease (Colletotrichum kahawae). In addition, nine morphological and agronomic traits were evaluated to determine the components of variance, select superior hybrids, and estimate genetic gain. From the genotypes evaluated, 134 were confirmed as hybrids. The genetic diversity between and within populations was 75.5% and 24.5%, respectively, and the cluster analysis revealed three primary groups. Pyramiding of CLR and CBD resistance genes was conducted in 11 genotypes using MAS. A selection intensity of 30% resulted in a gain of over 50% compared to the original population. Selected hybrids with increased gain also showed greater genetic divergence in addition to the pyramided resistance alleles. The strategies used were, therefore, efficient to select superior coffee hybrids for recurrent selection programs and could be used as a source of resistance in various crosses.

NEW SELECTION TECHNIQUES TO DETECT SOURCES OF RESISTANCE AGAINST STRIPE RUST IN WHEAT

Stripe rust is the most important biotic constraint in wheat production. Deployment of resistant wheat cultivars is the most practical way to decrease yield losses attributed to stripe rust. Usage of wild germplasm of wheat is the best technique to detect new resistant genes for the evolution of new varieties and mainstream of these hold capacity for disease resistance. Traditional procedures of gene identification by using conventional screening through diversified races do not generate accurate data. In conventional breeding, transferring desired traits, for instance, stripe rust resistance, from a donor parent is offered into a genotype of interest, typically high yielding. Identification of the sources of resistance by conventional screening through diversified races and backcross breeding is time-consuming which could be avoided through the usage of DNA markers. Marker-assisted selection (MAS) is practiced for the improvement of a variety of traits in wheat around the world through introgression of disease resistance against diseases including stripe rust, which may in any case partially support in providing the anticipated result. MAS has been valuable for the development of quite a lot of significant traits such as resistance against diseases. Marker-assisted backcrossing, forward breeding, and MAS involving doubled haploid technology have been effectively used for this objective. Novel skills based on high throughput genotyping related with new marker systems (e.g., Diversity arrays technology DArT and as Single Nucleotide Polymorphism SNP), and new selection strategies such as (Advanced backcross QTL AB-QTL), mapping-as-you-go, marker-assisted recurrent selection, and genome-wide selection will have to be tried in future for upgrading of compound multigenic traits. The improvement made in all these features of marker-assisted wheat breeding, and the restrictions and future scenarios of this incipient technology have been reviewed in this article.

Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review

Genomics is the study of the complete genetic material of an organism. It would not be an exaggeration to say that we are at the peak of the genomics era as with the advent of high-throughput sequencing technologies we have an enormous amount of genomic data coming every day. Genomics assisted breeding (GAB) is becoming increasingly popular in the field of crop improvement. GAB utilizes available genomics information of different crops and their relatives for the purpose of plant breeding to produce improved varieties of the crops. Proper knowledge of these tools and databases helps in speeding up the process of plant breeding. The available tools can be categorized into several groups such as genetic diversity, Quantitative Trait Locus (QTL)/gene mapping, Next-Generation Sequencing (NGS) based Single Nucleotide Polymorphism (SNP) genotyping, Molecular breeding, Genome-Wide Association Studies (GWAS), Genomic Selection (GS), Marker-Assisted Recurrent Selection (MARS), Multiparent Advanced Generation Inter-Cross (MAGIC), etc. Most of the available tools are user friendly and where it is not, needs to be updated soon. There is an urgent need to develop the scientific resources and technical expertise for the proper and effective use of these tools. In this review, we have extensively covered the available tools and databases for the genomic assisted breeding and population genetics study of the plants. The details of these tools and databases along with their web links are also provided. We believe this review will be handy and useful for the scientists and researches of plant breeding, population genetics, and genomics.

Enhancing genetic gains through marker-assisted recurrent selection: from phenotyping to genotyping

Enhancing genetic gains through marker-assisted recurrent selection: from phenotyping to genotyping

Improving Quantitative Traits in Self-Pollinated Crops Using Simulation-Based Selection With Minimal Crossing.

Genomic selection and marker-assisted recurrent selection have been applied to improve quantitative traits in many cross-pollinated crops. However, such selection is not feasible in self-pollinated crops owing to laborious crossing procedures. In this study, we developed a simulation-based selection strategy that makes use of a trait prediction model based on genomic information to predict the phenotype of the progeny for all possible crossing combinations. These predictions are then used to select the best cross combinations for the selection of the given trait. In our simulated experiment, using a biparental initial population with a heritability set to 0.3, 0.6, or 1.0 and the number of quantitative trait loci set to 30 or 100, the genetic gain of the proposed strategy was higher or equal to that of conventional recurrent selection method in the early selection cycles, although the number of cross combinations of the proposed strategy was considerably reduced in each cycle. Moreover, this strategy was demonstrated to increase or decrease seed protein content in soybean recombinant inbred lines using SNP markers. Information on 29 genomic regions associated with seed protein content was used to construct the prediction model and conduct simulation. After two selection cycles, the selected progeny had significantly higher or lower seed protein contents than those from the initial population. These results suggest that our strategy is effective in obtaining superior progeny over a short period with minimal crossing and has the potential to efficiently improve the target quantitative traits in self-pollinated crops.

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.

Marker assisted recurrent selection for genetic male sterile population improvement in rice

In the present study, by deploying marker assisted recurrent selection (MARS) strategy, the improvement of IR58025B genetic male sterile maintainer population for drought and salinity tolerance was carried out to develop maintainers with drought and salinity tolerance. Individual crosses were performed among sterile plants of IR58025B maintainer population and donors of drought tolerance viz., Vandana (qDTY12.1) and FL478 (Saltol). F1 plants were confirmed for the presence of target genes/QTLs with the help of SSR markers and raised to produce F2 seeds. Selected F 2 plants were harvested and seeds from each cross combination were mixed in equal proportions to generate population for the first random mating or recurrent selection cycle. The same process is continued up to 4th cycle and 200 selected plants were subjected to genotyping for drought and salinity with the help of reported SSR markers. About 48 plants were found positive for salinity tolerance, 17 plants were positive for drought and 10 plants were positive for both the traits. These lines were advanced by pedigree method of breeding for deriving maintainers with drought and salinity tolerance.

Genome-Wide Association Analysis of Fusarium Head Blight Resistance in Chinese Elite Wheat Lines.

Fusarium head blight (FHB) is a devastating wheat disease worldwide. To decipher the genetic architecture of FHB resistance in Chinese germplasm, a Wheat Association Panel for Scab Research (WAPS) consisting of 240 leading Chinese wheat cultivars and elite lines was genotyped using the 90K single nucleotide polymorphism (SNP) arrays. The FHB response was evaluated in the field nurseries in Wuhan in Hubei Province over four consecutive years from 2014 to 2017. Five quantitative trait loci (QTL) were consistently identified on chromosome arms 1AS, 2DL, 5AS, 5AL, and 7DS using a mixed linear model (MLM), explaining 5.6, 10.3, 5.7, 5.4, and 5.6% of phenotypic variation, respectively. The QTL on 5AS, 5AL, and 7DS QTL are probably novel. The allelic frequency analysis indicated that cultivars from the Middle and Lower Yangtze River Valleys harbored more favorable alleles and were therefore more resistant than those from other regions. To facilitate in-house germplasm screening and marker-assisted selection (MAS), SNP-derived PCR markers were developed for the QTL regions on 1AS, 5AS, and 5AL QTL. In addition to the above five QTL, the WAPS population had a very low frequency of Fhb1, confirming that the gene is not widely used in Chinese wheat breeding programs. The resistant lines and molecular markers developed in this study are resources and information for enhancing FHB resistance in breeding populations by marker-assisted recurrent selection and gene stacking.

Marker-assisted recurrent selection improves the crown rot resistance of bread wheat

Crown rot of wheat and barley is a serious disease caused by the fungus Fusarium pseudograminearum, a stubble-borne pathogen common in no-till farming systems in water-limited grain growing regions. Marker assisted recurrent selection (MARS) was used to more effectively pyramid minor genes controlling plant response to crown rot disease. Two populations comprising 475 genotypes were phenotyped for adult plant resistance and genotyped using a 9K SNP array. A genome-wide association study (GWAS) was used to estimate quantitative trait locus (QTL) effects as more than two parents were recombined in each population. A total of 23 significant and unique marker-trait associations (MTAs) were identified in both populations. A Kompetitive allele-specific PCR (KASP) assay was developed and used to genotype the progeny and parents of each recombination cycle. Following two cycles of recombination among progeny, up to 22 markers of a possible 23 were recombined. Two hundred ninety-seven double haploid-derived lines representing both cycles of recombination, the original parents, parents selected from the base population and local cultivars were evaluated for crown rot resistance in 2016 and 2017 in the field under crown rot inoculation pressure. A significant and positive response to each cycle of recurrent selection was observed. MARS was an effective breeding strategy for combining many QTLs of small effect for crown rot resistance in wheat.

Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

Key messageSNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F1 progeny of a segregating population.Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.

Genetics of Fe, Zn, β-carotene, GPC and yield traits in bread wheat (Triticum aestivum L.) using multi-locus and multi-traits GWAS

The present study was conducted to study the genetic architecture of grain micronutrients (Zn, Fe and β-carotene contents), grain protein content and four yield traits in a spring wheat reference set comprising 246 genotypes. Phenotypic data on these traits recorded at two locations and the genotyping data for 17,937 SNP markers (obtained through outsourcing) were used for genome wide association study, which gave following results after Bonferroni correction using four methods: (1) single locus single trait analysis gave 136 marker-trait associations; (2) multi-locus mixed model gave 587 MTAs; (3) multi-trait mixed model gave 28 MTAs and (4) matrix-variate linear mixed model gave 33 MTAs. As many as 73 epistatic interactions were also detected. Keeping all the results in mind, nine most important MTAs were selected for biofortification. These markers were associated with three traits (GPC, GFeC and GYPP). These MTAs can be used in wheat improvement programs either using marker-assisted recurrent selection or pseudo-backcrossing method.

Positive interactions of major-effect QTLs with genetic background that enhances rice yield under drought

To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY2.2 + qDTY4.1 in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY1.1 + qDTY2.1 + qDTY3.1 + qDTY11.1) and two QTLs (qDTY1.1 + qDTY11.1) yielded higher than PLs with other qDTY combinations. The selected PLs showed a yield advantage of 0.3–2.0 t ha−1 under RS. An allelic profile of MAS PLs having same qDTY combination but with different yields under drought was studied. Hierarchical clustering grouped together the selected lines with high yield under drought. Epistasis test showed the interaction of qDTY4.1 and qDTY9.1 loci with qDTY7.1 significantly increased yield under drought and all the lines with higher yield under drought possessed the conserved region of qDTY7.1 on chromosome 7. The positive interactions among QTLs, effectiveness of QTLs in different backgrounds, introgression of DTY QTLs together with resistance to biotic stresses shall help enhance grain yield under RS.

QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments.

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.

Genetic Dissection of Seedling Stage Salinity Tolerance in Rice Using Introgression Lines of a Salt Tolerant Landrace Nona Bokra.

Salinity is an important abiotic stress affecting rice production worldwide. Development of salt tolerant varieties is the most feasible approach for improving rice productivity in salt affected soils. In rice, seedling stage salinity tolerance is crucial for better crop establishment. Quantitative trait loci (QTL) mapping using introgression lines (ILs) is useful for identification and simultaneous transfer of desirable alleles into elite genetic background. In the present study, 138 ILs derived from the cross between a high yielding elite salt susceptible japonica rice cultivar Jupiter and a salt tolerant indica landrace Nona Bokra were evaluated for salt tolerance at seedling stage in a hydroponics experiment and were genotyped using 126 simple sequence repeat markers. A total of 33 additive QTLs were detected by composite interval mapping for 8 morphophysiological traits. The phenotypic responses, genomic composition, and QTLs identified from the study indicated that Na/K ratio is the key factor for salinity tolerance. The mechanisms of tolerance might be due to homeostasis between Na+ and K+ or Na+ compartmentation. Gene ontology (GO) analysis revealed that significant GO terms in the selected QTL regions were associated with the genes/pathways involved in signaling, enzyme inhibition, and ion transport. Because majority of QTLs are with small effects, marker-assisted recurrent selection is proposed to accumulate favorable alleles for improving salt tolerance using the tolerant ILs identified in this study. The tolerant ILs also provide an opportunity for functional genomics studies to provide molecular insights into salt tolerance mechanisms in Nona Bokra.