Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the ‘Legume Federation’ project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.

Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to identify quantitative trait loci (QTL) for vegetative stage tolerance to heat stress in rice and the corresponding candidate genes. We used genotyping-by-sequencing to generate single nucleotide polymorphic (SNP) markers and genotype 150 F8 recombinant inbred lines (RILs) obtained by crossing heat tolerant “N22” and heat susceptible “IR64” varieties. A linkage map was constructed using 4,074 high quality SNP markers that corresponded to 1,638 recombinationally unique events in this mapping population. Six QTL for root length and two for shoot length under control conditions with 2.1–12% effect were identified. One QTL rlht5.1 was identified for “root length under heat stress,” with 20.4% effect. Four QTL were identified for “root length under heat stress as percent of control” that explained the total phenotypic variation from 5.2 to 8.6%. Three QTL with 5.3–10.2% effect were identified for “shoot length under heat stress,” and seven QTL with 6.6–19% effect were identified for “shoot length under heat stress expressed as percentage of control.” Among the QTL identified six were overlapping between those identified using shoot traits and root traits: two were overlapping between QTL identified for “shoot length under heat stress” and “root length expressed as percentage of control” and two QTL for “shoot length as percentage of control” were overlapping a QTL each for “root length as percentage of control” and “shoot length under heat stress.” Genes coding 1,037 potential transcripts were identified based on their location in 10 QTL regions for vegetative stage heat stress tolerance. Among these, 213 transcript annotations were reported to be connected to stress tolerance in previous research in the literature. These putative candidate genes included transcription factors, chaperone proteins (e.g., alpha-crystallin family heat shock protein 20 and DNAJ homolog heat shock protein), proteases, protein kinases, phospholipases, and proteins related to disease resistance and defense and several novel proteins currently annotated as expressed and hypothetical proteins.

Maternal control of seed size in the common bean provides an opportunity to study genotype-independent seed weight effects on early seedling growth and development. We set out to test the hypothesis that the early heterotrophic growth of bean seedlings is determined by both the relative amount of cotyledon storage reserves and the genotype of the seedling, provided the hybrid genotype could be fully expressed in the seedlings. The hypothesis was tested via comparison of seed weight and seedling growth phenotypes of small-seeded (wild, ~0.10 g) and large-seeded (landrace, ~0.55 g) parents and their reciprocal F1 hybrids. Akaike's Information Criteria were used to estimate growth parameters and identify the phenotypic model that best represented the data. The analysis presented here indicates that the hybrid embryo genotype is not fully expressed during both seed and seedling growth and development. The analysis presented here shows that seed growth and development are controlled by the sporophyte. The strong similarity in seed size and shape of the reciprocal hybrid seed with seeds of the maternal parents is evidence of this control. The analysis also indicates that since the maternal sporophyte controls seed size and therefore the amount of cotyledon reserves, the maternal sporophyte indirectly controls early seedling growth because the cotyledons are the primary nutrient source during heterotrophic growth. The most interesting and surprising results indicated that the maternal effects extended to the root architecture of the reciprocal hybrid seedlings. This phenomenon could not be explained by seed size, but by alterations in the control of the pattern of gene expression of the seedling, which apparently was set by a maternally controlled mechanism. Although seed weight increase was the main target of bean domestication, it also had positive repercussions on early-growth traits and stand establishment.

We present here the first comprehensive genetic characterization of wild melon accessions from northern India. The genetic diversity among 43 wild melon accessions collected from the six agro-ecological regions of the Punjab State of India was assessed by measuring variation at 16 Simple Sequence Repeat (SSR) loci, morphological traits of plant habit and fruit morphological traits, two yield-associated traits, root nematode resistance and biochemical composition (ascorbic acid, carotenoids, titrable acidity). Variation among accessions was observed in plant habit and fruit traits and wild melon germplasm with high acidity and elevated carotenoid content and possessing resistance to Meloidogyne incognita was identified in the collection. A high level of genetic variability in wild melon germplasm was suggested by SSR analysis. Comparative analysis using SSRs of the genetic variability between wild melons from the north and other melons from the south and east regions of India and also reference accessions of cultivated melon from Spain, Japan, Korea, Maldives, Iraq and Israel, showed regional differentiation among Indian melon accessions and that Indian germplasm was not closely related to melon accessions from other parts of the world. A highly drought tolerant accession belonging to var. agrestis Naud. was also identified.

Summary Pear ( Pyrus ; 2 n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny in a timely and cost‐effective manner. Genotyping arrays can provide fast, efficient and high‐throughput genetic characterization of diverse germplasm, genetic mapping and breeding populations. We present here 200K AXIOM ® Pyr SNP , a large‐scale single nucleotide polymorphism ( SNP ) genotyping array to facilitate genotyping of Pyrus species. A diverse panel of 113 re‐sequenced pear genotypes was used to discover SNP s to promote increased adoption of the array. A set of 188 diverse accessions and an F 1 population of 98 individuals from ‘Cuiguan’ × ‘Starkrimson’ was genotyped with the array to assess its effectiveness. A large majority of SNP s (166 335 or 83%) are of high quality. The high density and uniform distribution of the array SNP s facilitated prediction of centromeric regions on 17 pear chromosomes, and significantly improved the genome assembly from 75.5% to 81.4% based on genetic mapping. Identification of a gene associated with flowering time and candidate genes linked to size of fruit core via genome wide association studies showed the usefulness of the array in pear genetic research. The newly developed high‐density SNP array presents an important tool for rapid and high‐throughput genotyping in pear for genetic map construction, QTL identification and genomic selection.