10 CONTEMPORARY SELECTION PARADIGMS FOR ENHANCING QUALITATIVE AND
QUANTITATIVE PRODUCTIVE TRAITS IN CROPS
Shiv Om Pratap1, Ruchi Gaur2 and J.L Bhat2
Department of Biotechnology, Christian Eminent College, Indore (M.P) ITM University, Gwalior
Abstract - Human remained depend on plants and their products for their survival from the beginning of agricultural practices across ancient Indian farming system via conventional breeding manage mental programs via selection of an efficient host for the preparation of seeds to carry out the next crops. The concept of breeding was introduced at the same time by incorporating the germ-plasm of two selected parental cells for the preparation of hybrid seeds to enhanced productivity by inculcating the multiple traits like as; disease resistance, drought, temperature tolerance etc. Molecular markers are advent tools for the assessment of biological diversity of plant species due to low investment cost as against manually selection, reliable estimates through analytical statistical tools, expediency and reproducibility which remain in favor of MAS based selection program to characterize the larger number of germplasm with minimal time and resources. These Molecular markers are ease in recognition for almost possible phenotypes, efficient rate of expression, allele specificity, ability of segregating in mendelian way, polymorphic, reproducibility to screen genetic diversity having great significances in the Agricultural Biotechnology for enhancing our cropping system. MAS based selection programs is found more beneficial as compare to earlier methods of selection during the conventional farming system upon the basis of unique alleles across the genome for the establishment of more efficient hybrids for the determination of desired traits.
Keywords: Genetic diversity, molecular marker, breeding, selection, QTL, hybrid etc.
1 INTRODUCTION
To meet with the required food for growing population after independence, various revolutions such as; „Green revolution for elevated yield of cereals, Yellow Revolution to attain the maximum productivity of oilseeds, Operation flood to dairy products and Blue revolution for fishery have been used (Pratap et. al., 2022). Significant growth was registered in the agricultural sector, with utilization of synthetic fertilizers but also caused infertility, erosion, disturbing the pH and physical and chemical characterizations of soil due to the extensive use of these Chemical fertilizers for increased productivity for the growing population (Pratap et. al., 2022). Organic farming by organic compost from biological waste, using of conventional seeds, systematic progression of cropping cycles have been employed earlier in ancient India for the clean and green production methods without the use of chemical fertilizers and pesticides but could not meet with the expected yield for the growing population and even in adverse environmental conditions like;
extreme hot, dry and raining which caused more loss to the cropping yield. During the plant breeding, genetic variability play an important role for the development of new cultivars via multiple crosses like test cross and back cross.
With the increasing population and decreasing fertile land area, various measures have been adopted to meet with the demand of nutritious food to population, strategies are now focusing for enhancing qualitative and quantitative traits of crops by employing advent tools like as; Molecular breeding, Protoplast technology, Tissue culture, Genetic Engineering, Site Directed Mutagenesis, Molecular Marker System etc. to meet with the challenges of higher productivity of cropping system as compare to conventional methods were used traditionally in ancient India (Frona et. al., 2010). The success of breeding programs depend upon the fact that how much efficient strain/host has been selected either on phenotypes basis or existence of specific genotype by molecular marker system known as Marker-assisted selection (MAS) program which is a highly versatile tool in modern era of Biological Sciences due to its ability to find out the genetic diversity within or between the species for enhanced productivity, especially in case of wheat and rice (Pratap et. al., 2022).
11 DNA based genetic markers found associated with multiple genes can delineate the efficient selection of a best host plant for the further breeding regimens. MAS includes, selection of desired traits such as; abiotic stresses, disease resistance, productivity etc through the utilization of Biochemical, Morphological and robust DNA marker system for selection programs globally for breeding strategies through the identification of desired QTL and Linkages among the genome (Salgotra et. al., 2020). Marker assisted selection or marker aided selection (MAS) is an indirect selection process as compare to earlier used conventional selection methods upon the basis of growth, height, productivity etc.. During MAS, selection has carried out on the existence of unique alleles or sequences where a trait of interest is selected with the help of molecular marker like as; morphological, biochemical or DNA/RNA found associated linked to a trait of interest (e.g. productivity, disease resistance, abiotic stress tolerance, and quality), rather than observational conventional methods. (Pratap et. al., 2022, Salgotra et. al., 2014).
Marker-assisted Recurrent Selection (MARS) is a special breeding procedure used for finding out unique alleles across the genome. DNA markers encompass potential for improving the efficiency of earlier conventional selection procedures through MAS regimens and not affected by the environmental factors.
Various quantitative trait loci (QTLs) with the help of plant genome mapping studies have unravel multiple trait marker association (David et. al., 2008). Traditional plant breeding is selection of phenotypic based selection procedure for identifying the best host genotype plant breeding, genetic variability is the base for the improvement and the development of new cultivars. Genetic variability is repetitively produced in crosses and selections for desired traits.
2 HISTORY OF MOLECULAR MARKER DEVELOPMENT
With the genomic evolution, the sequencing gave us a well understanding about the genetic make-up of an individual in 1990s. With the recent advances of molecular markers system various QTLs have identified (Anom et. al., 2014). Various types of Molecular markers have discovered like as:; amplified length polymorphism (AFLP), Random Amplified polymorphism DNA (RAPD), Microsatellites or simple sequence repeat (SSR), Single Nucleotide Polymorphism (SNP), Diversity Array (DArT), Sequence Characterized Amplified Region (SCARs) have discovered with some advantages and disadvantages ( Botstein et. al., 1980; William et. al., 1990; Welsh et. al., 1990; Vos et. al., 1989; Tautz et. al., 1989; Litt et. al., 1989 ). Another approach, functional markers ( FMs) in genetic regions are found directly linked with certain phenotypic traits and variations (Andersen, et. al., 2003) and known as precision markers or diagnostic markers which facilitate rapid categorization of germ-plasm for allelic diversity in targeted breeding population (Varshney et al., 2005;
Anderson et. al., 2003).
2.1 Classification of Molecular Markers:
These markers have classified in various classes upon the basis of their mode of working, utilization and applications such as:
a) Classical Markers:
Morphological Markers can visually differentiate the qualitative traits such as; height, growth traits, structural features, flowers, growth parameters, seed morphogenesis etc.
They do not need any specific scientific knowledge of markers or tools and techniques for the selection of a best host (Karakoy et. al., 2014).
b) Cytological Markers:
These are the types of Markers found based on genetic variabilities like as; banding prototypes, size, shape, order and chromosomal locations (Zang et al., 2013).
c) Biochemical Markers:
These are the various types of subunits of enzymes which encode by the specific genes encompasses almost similar functions. They are allelic variations of enzymes and thus gene and genotypic frequencies can be estimated with biochemical markers. Biochemical
12 markers have been successfully applied in the detection of genetic diversity, population structure, gene flow (Bayley et. al., 1983).
d) Genetic Markers:
The Markers consist a stretches of nucleotide segment or DNA sequences for the detection of specific genes in the host genome and very important for the agricultural crops as RAPD, AFLP, RFLP, SNPs, SSRs etc. These Markers also can be classified in to PCR based markers like as SNPs, Microsatellite or SSRs, AFLP and Hybridization based markers such as RFLP.
3 MECHANISM OF MOLECULAR MECHANISM
These molecular Markers are found codominant, reproducible, higher polymorphic, linkage with traits of economic importance, need minute amount of DNA and inherited together (Pratap et. al., 2016). Molecular marker polymorphism occurs due to the mutations across the genome which produced the genetic differences among the individuals (Lincoln et al., 2018). Marker polymorphisms in the host are caused by point mutations due to change in the single nucleotides substitutions, rearrangements involving insertions or deletions, duplication, tandem repeats translocations and inversions as well as false or mutated DNA.
(Selvakumari et al., 2017). Genetic markers can aid in the development of new novel traits that can be put into mass production. These novel traits can be identified using molecular markers and maps. Particular traits such as color, may be controlled by just a few genes.
Once a desired marker has traced, than it will be able to be use within different filial generations. An identifiable marker may be help full particular to traits of interest when crossing between different genus or species.
Table 1 Distinguished nature of Molecular markers Types of
Markers PCR
Based Mode of
inheritance Locus
specificity Polymorphic
nature Reproducibility
RFLP No Co-dominant Yes Low-Medium High
RAPD Yes Dominant No Medium-High Low
SCAR Yes Co-dominant Yes High High
AFLP Yes Dominant No High Medium
SSR Yes Co-dominant Yes High High
ISSR Yes Dominant Yes High Medium
SNP Yes Co-dominant Yes Extremely
High High
DArT No Dominant Yes High High
The mode of molecular markers is found as follows-
13 3.1 Expression of DNA Marker
The steps for allelic expression are as follows:
Isolation of DNA from the selected tissue from the targeted population, selection of a DNA markers for the study, PCR profiling of targeted alleles, electrophoresis or sequencing for the confirmation of desired alleles, study of Marker-trait association for the gene of interest, data analysis, profiling of marker- trait association, section the best host population upon the basis of Marker data analysis, breeding regimen or policies for the propagation of desired population further.
3.2 Advantages of Molecular Markers for MAS:
DNA markers got attention globally for effective implementation of MAS program by having many advantages like as; can be use on the seeds, not affected by the environmental factors, recessive alleles may be used, cost effective, accurate, reliable, co- dominance in nature, quicker as compare to phenotypic selection, reproducible, minute amount of DNA needed for PCR typing etc.
3.3 Disadvantages of Molecular Markers:
Some drawbacks are also found associated with the Molecular Markers such as; needed more scientific knowledge, may be more expensive due to requirement of large investment of laboratory instruments, false expression of alleles due to recombination of marker and targeted genes, sometimes marker remained unable to detect the locus of a genes etc.
4 SUMMARY
MAS has already confirmed the precious results for the introgression of important genes into the parents of elite species through both foreground and background selections.
Such type of experiments always produces new gene recombinants and linked markers for traits of economic importance identification and confirmation with the help of recent tolls and techniques.
For example, MAS has utilized in the wheat population for more than 20 trait- associated markers. DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). Knowledge of actual gene sequences and design of PCR primers for specific alleles will make MAS more powerful and informative across a range of genetic backgrounds. Ongoing developments in statistical tools and techniques, effective experimental plans definitely will enhance the efficacy of MAS for multiple breeding population. The incorporation of MAS with QTLs analysis would be a rational approach. Efficient incorporation of MAS into an applied breeding program will likely require a rethinking of the structure and implementation of the entire program. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.
In summary, MAS is a methodology that has already proved its valuable informations in various plant breeding program. It is likely to become more valuable as a larger number of genes are identified and their functions and interactions elucidated. In future, minimal cost, standard procedure, integrated approaches for enhancing the efficacy of MAS based breeding regimens will definitely help in the optimum selection program which needs in- depth study further.
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