Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees.

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Impacts of public policies and farmer preferences on agroforestry practices in Kerala, India.

Agroforestry systems are fundamental features of the rural landscape of the Indian state of Kerala. Yet these mixed species systems are increasingly being replaced by monocultures. This paper explores how public policies on land tenure, agriculture, forestry and tree growing on private lands have interacted with farmer preferences in shaping land use dynamics and agroforestry practices. It argues that not only is there no specific policy for agroforestry in Kerala, but also that the existing sectoral policies of land tenure, agriculture, and forestry contributed to promoting plantation crops, even among marginal farmers. Forest policies, which impose restrictions on timber extraction from farmers' fields under the garb of protecting natural forests, have often acted as a disincentive to maintaining tree-based mixed production systems on farmlands. The paper argues that public policies interact with farmers' preferences in determining land use practices.