Subsistence Farming, Agrobiodiversity, and Sustainable Agriculture: A Case Study

<div><p>Subsistence farming still predominates in many places across the globe including India. Crops and livestock are often integral key components of subsistence farming practiced generally by smallholder farmers. A precise documentation of traditional farming practices involving native diversity with overall objectives of their conservation and showcasing their role in addressing livelihood security of farmers was done in the present study. This case study was undertaken in three underprivileged districts of India representing specific agroecosystems. The outcome of the study could help develop a policy framework for bringing sustainable agricultural development to subsistence farming agroecosystems. It could also help in exploring and advocating the potential of various suggested “add-value” interventions to native agrobiodiversity in addressing livelihood security of farmers.</p></div

Population structure of the combined samples of North-eastern India and global rice cultivars.

<p>(<b>a</b>) Model-based population assignment using STRUCTURE analysis. (<b>b</b>) NJ tree based on C. S. Chord genetic distance. (<b>c</b>) Principal coordinate analysis.</p

Genetic Diversity and Population Structure in Aromatic and Quality Rice (<i>Oryza sativa</i> L.) Landraces from North-Eastern India

<div><p>The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, <i>joha</i> rice accessions from Assam, <i>tai</i> rices from Mizoram and those from Sikkim; P2, <i>chakhao</i> rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise <i>F_ST</i> between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (<i>Indica</i> and <i>Japonica</i>) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the <i>Indica</i> group, while the accessions from Nagaland exhibited close association with <i>Japonica</i>. The <i>tai</i> accessions of Mizoram along with few <i>chakhao</i> accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice germplasm of NE India for rice improvement.</p></div

Analysis of molecular variance of aromatic and quality rice landraces of North-eastern India.

<p>Notes: df, Degrees of freedom, SS, Sum of squares, CV, Variance component estimates, % Total, percentage of total variation.</p><p>Analysis of molecular variance of aromatic and quality rice landraces of North-eastern India.</p

Population structure of 107 aromatic and quality rice accessions of North-eastern India.

<p>(<b>a</b>) Model-based clustering using STRUCTURE analysis. (<b>b</b>) NJ tree based on C. S. Chord genetic distance. (<b>c</b>) Principal coordinate analysis.</p

Summary statistics of microsatellite diversity in 107 aromatic and quality rice landraces of North-eastern India.

<p>Notes: N, Number of accessions; AN, Number of allele per locus; <i>H</i>_<i>e</i>, Gene diversity or expected heterozygosity; <i>H</i>_<i>o</i>, Observed heterozygosity; PIC, Polymorphism information content.</p><p>Summary statistics of microsatellite diversity in 107 aromatic and quality rice landraces of North-eastern India.</p

Summary statistics of the 40 SSR markers used in this study.

<p>Notes:</p><p>*Taken from panel of 50 standard SSR markers: <a href="http://archive.gramene.org/markers/microsat/50_ssr.html" target="_blank">http://archive.gramene.org/markers/microsat/50_ssr.html</a>.</p><p>^†SSR markers selected for combined analysis of current genotyping data and global rice germplasm data reported in Garris et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129607#pone.0129607.ref003" target="_blank">3</a>].</p><p>Chr, Rice chromosome; AN, Number of allele per locus; <i>H</i>_<i>e</i>, Gene diversity or expected heterozygosity; <i>H</i>_<i>o</i>, Observed heterozygosity; PIC, Polymorphism information content.</p><p>Summary statistics of the 40 SSR markers used in this study.</p

Geographical location of North-eastern region of India.

<p>The collection sites of rice landraces are indicated by circles. Smaller and bigger dots denote the collection sites with and without actual geographical coordinates, respectively.</p

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases

<div><p>A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–<i>Triticum aestivum</i>, <i>T</i>. <i>durum</i> and <i>T</i>. <i>dicoccum</i> were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.</p></div

Seedling resistance in wheat accessions.

<p>These genebank accessions were identified as resistant in the primary field evaluation at the hotspots. The seedling resistance was recorded as resistant either to only one rust disease (leaf, stem or stripe) or a combination of two or all the three rust diseases. Seedling resistance screening was carried out under controlled condition at the Regional Station of Indian Institute of Wheat and Barley Research (IIWBR), Flowerdale, Shimla. Accession-wise details are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167702#pone.0167702.s003" target="_blank">S3 Table</a>.</p