Preprocessing Tools for Data Preparation

This data preparation chapter is of paramount importance for implementing statistical machine learning methods for genomic selection. We present the basic linear mixed model that gives rise to BLUE and BLUP and explain how to decide when to use fixed or random effects that give rise to best linear unbiased estimates (BLUE or BLUEs) and best linear unbiased predictors (BLUP or BLUPs). The R codes for fitting linear mixed model for the data are given in small examples. We emphasize tools for computing BLUEs and BLUPs for many linear combinations of interest in genomic-enabled prediction and plant breeding. We present tools for cleaning, imputing, and detecting minor and major allele frequency computation, marker recodification, frequency of heterogeneous, frequency of NAs, and three methods for computing the genomic relationship matrix. In addition, scaling and data compression of inputs are important in statistical machine learning. For a more extensive description of linear mixed models, see Chap. 10.1007/978-3-030-89010-0_5.

Morpho-molecular diversity study of rice cultivars in Bangladesh

Rice is one of the frontline cereals in the world and the major cultivated crop in Bangladesh. A total of eleven simple sequence repeats (SSRs) and thirteen sequence-tagged site (STS) markers were used to characterize twenty-four rice cultivars in Bangladesh. Twenty-four markers generated 60 alleles with 2.5 alleles per locus. The average polymorphism information content (PIC) value was 0.40, while the mean value of heterozygosity, gene diversity, and major allele frequency were recorded as 0.10, 0.48 and 0.62, respectively. However, the SSR markers showed more specificity and a higher discrimination power than the STS markers. The cluster analysis displayed four major clusters with a genetic similarity coefficient value of 0.73. The morphological analyses of the grain identified that Binadhan-20 and BRRI dhan34 had the longest and the shortest seed size, respectively, with a variable correlation between the seed length, width and length/width ratio. The phenol reaction test distinguished seven cultivars as japonica and seventeen cultivars as indica or an intermediate type. All these results regarding the phenotypic data and marker information will be useful for parental selection in modern rice breeding programmes.

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies.

Evaluation of Diversity among Soybean Genotypes via Yield Attributing Traits and SSR Molecular Markers

Introduction: As an important source of nutrients to humans and animals, soybean is considered to be a major crop. Objective: The present study has been executed to identify diverse soybean genotypes on account of different morpho-physiological and microsatellite molecular markers. Study Design: Data for Morpho-physiological traits were recorded from experiment conducted under field conditions in RBD design whereas molecular work was conducted in Laboratory. Place and Duration of the Study: The present study was conducted at College of Agriculture, Gwalior, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, M.P., India during Kharif 2018-19. Methodology: The study was conducted to document different morphological and physiological traits related to the yield and its attributing traits in soybean. Total 32 microsatellite markers were also used in laboratory to analyze the variability among soybean genotypes. Results: Morpho-physiological analysis among 53 genotypes revealed the presence of considerable level of variability. Phylogenetic tree based on morpho-physiological traits grouped the genotypes into major and minor cluster. Major cluster had fifty genotypes while minor cluster had only three genotypes. Among polymorphic 32 microsatellite markers, the highest genetic diversity (0.66) was recorded in Satt520 whilst lowest (0.037) was in Satt557 with an average of 0.35. The highest PIC value was 0.59 prearranged by Satt520 and lowest 0.036 by Satt557. An average major allele frequency was 0.69 while, an average PIC value was 0.32. Microsatellite markers-based data also grouped the genotypes into one major and one minor cluster. Conclusion: Molecular analysis based on microsatellite markers confirms the presence of genetic variability among genotypes under the investigation. Data obtained in the present investigation may contribute towards improvement of soybean genotypes to develop high yielding varieties by considering diverse genotypes with good agronomical traits in hybridization programme.

Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus)

Agaricus bisporus is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the A. bisporus genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 A. bisporus accessions for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0–0.499 (mean = 0.265) and 0.0–0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with F-statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299–0.499) and major allele frequency (MAF, range 0.524–0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.

Screening of Pearl Millet [Pennisetum glaucum (L.) R. Br.] Germplam Lines for Drought Tolerance Based on Morpho-physiological Traits and SSR Markers

Aim: The present study was undertaken to analyze genetic diversity among pearl millet genotypes based on drought linked morpho-physiological and microsatellite markers. Study Design: In the present investigation, 96 pearl millet germplasm lines were screened against drought using different morphological and physiological traits along with SSR markers. Place and Duration of the Study: The present study was conducted at College of Agriculture, Gwalior, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, M.P., India during July 2019 to December, 2020. Methodology: The study was conducted to record different morphological and physiological traits related to drought tolerance and susceptibility. Thirty five microsatellite markers were also used in laboratory to analyze the variability among pearl millet genotypes under study. Results: Pearl millet genotypes were grouped according to their morpho-physiological characteristics. Among 35 SSR markers, twenty-two were successfully amplified across all germplasm lines and seven SSR markers were found to be polymorphic and fifteen markers were monomorphic. All seven polymorphic SSR markers were used consequently for amplification of all the 96 germplasm lines. The range of PIC value was 0.0939 to 0.2980 with the average of 0.2274. The highest PIC value was recorded for the markers Xibmsp26 and Xibmsp29 (0.2980), followed by Xibmsp03 (0.2392), Xibmsp29 (0.2392), Xibmsp06 (0.2289) and Xibmsp07 (0.1948) while the lowest for the marker Xibmsp01 (0.0939). The range of major allele frequency value was 0.7604 to 0.9479 with the average of 0.8363. The range of genetic diversity value was 0.0987 to 0.3644 with the average of 0.2665. Conclusions: According to the morpho-physiological data a total of 22 pearl millet genotypes were found to be grouped distantly from rest of the genotypes. These genotypes had shown their drought tolerance bahaviour however, rests of the genotypes were found to be susceptible against drought.

Phylogenetic analysis of Colchicum (Colchicaceae) genus by molecular markers from nuclear and chloroplast genome

We evaluated the patterns of genetic variation of 16 Colchicum species, including 37 different genotypes, using RAPD marker and trnL–trnF chloroplast DNA sequence. A total of 861 polymorphic alleles through RAPDs showed a mean of 33.88 ± 3.80 alleles per primer, while mean major allele frequency was 0.067 ± 0.05. The sequence length of trnL–trnF ranged from 1022 bp to 1081 bp. The phylogenetic tree was constructed to understand the relationship between Colchicum species and the discrimination power of the nuclear and chloroplast genome for species. The results showed that trnL–trnF gene region grouped Colchicum species well in comparison with RAPD analysis. This data was also supported by haplotype network analysis, structure analysis and PCA (Principle Component Analysis). This study showed that there is a need for a characterization that contains more molecular and morphological methods to correctly distinguish Colchicum species.

Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis

Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao (Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (MiAF), polymorphism information content (PIC), and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, MiAF, and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.

Morphological and Molecular Characterization of Tropical Strawberry

The experiment was conducted to assess five tropical strawberry genotypes at phenotypic and molecular level. Among the five strawberry genotypes (BARI Strawberry 1, BARI Strawberry 2, BARI Strawberry 3, FA 005 and Festival), BARI Strawberry 2 was found to be the best in respect of fruit per plant (32.42), fruit yield per plant (594.73 gm) and yield per hectare (19.39 ton). Ten SSR primers were initially screened for molecular characterization and finally MFv104, ARSFL-10 and ARSFL-15 markers were selected for the analysis. EMFv104 and ARSFL-15 produced the maximum number of polymorphic alleles (4) while ARSFL-10 produced three polymorphic alleles. The major allele frequency at each locus ranged from 0.4 (EMFv104) to 0.6 (ARSFL-10). The PIC values varied from 0.4992 on ARSFL-10 to 0.672 on EMFv104. The gene diversity ranged from 0.56 (ARSFL-10) to 0.72 (EMFv104 and ARSFL-15). BARI Strawberry 1 and Festival were the closest genotypes with the lowest genetic dissimilarity value of 0.16667. EMFv104 and ARSFL-15 can be used as polymorphic markers for assessing genetic diversity of different strawberry genotypes.