Draft genomes of two Artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis)

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S.aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments

The draft genomes of five agriculturally important African orphan crops

Background: Continuous growth of the world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries current face a serious burden of malnutrition, especially in Africa and South and South-East Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize and rice provide the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition, greater use of neglected or underutilized local plants (so-called 'orphan crops‘, but also including a few plants of special significance to agriculture, agroforestry and nutrition) could be a partial solution.Results: Here, we present draft genome information from five agriculturally, biologically, medicinally and economically important underutilized plants native to Africa; Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea and M. oleifera we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes, respectively. By further analysing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors and starch biosynthesis-related genes in these genomes.Conclusions: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused and predictable crop improvement programs

Development of Genic and Genomic SSR Markers of Robusta Coffee (<i>Coffea canephora</i> Pierre Ex A. Froehner)

<div><p>Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic−/genomic-SSR markers using <i>in-silico</i> bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study.</p></div

Allelic diversity attributes of the newly developed 44 EST-SSRs when tested over cultivated and wild related coffee genera.

<p><b>Note</b>: N_A: Number of amplified alleles; PA: Number of Private Alleles; H_o: Observed heterozygosity; H_e: Expected heterozygosity; PIC: Polymorphism Information Content; PI: Probability of Identity; NA: Not amplified; *: Significant HW dis-equilibrium at P<0.05; **: Highly significant HW dis-equilibrium at P<0.01; The putative DL (duplicated loci) markers were not considered for calculation of various estimates as these appear to be fixed exhibiting no segregation.</p><p>Allelic diversity attributes of the newly developed 44 EST-SSRs when tested over cultivated and wild related coffee genera.</p

Details of the new genomic SSR markers developed using streptavidin-avidin affinity capture SSR-enriched library in the present study.

<p>CCRM: CCMB CXR Microsatellite marker;</p><p>T_a: annealing temperature;</p><p>F: forward primer;</p><p>R: reverse primer;</p><p>–: Unmapped;</p><p>CLG: Combined Linkage Group <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113661#pone.0113661-Hendre1" target="_blank">[1]</a>;</p><p>*: Expected amplicon size in the robusta variety CxR.</p><p>Details of the new genomic SSR markers developed using streptavidin-avidin affinity capture SSR-enriched library in the present study.</p

Details of the new EST-SSR markers developed using EST database and validated using diverse coffee genotypes in the present study.

<p>CCESSR: <b>C</b>CMB <b>C</b>offee <b>E</b>ST <b>SSR</b> marker;</p><p>F: forward primer;</p><p>R: reverse primer;</p><p>–: Unmapped;</p><p>CLG: Combined Linkage Group <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113661#pone.0113661-Hendre1" target="_blank">[1]</a>;</p><p>*: Predicted amplicon size based on source EST sequence;</p><p>**: Source EST ID as per the downloaded SGN database (<a href="ftp://ftp.sgn.cornell.edu/coffee/" target="_blank">ftp://ftp.sgn.cornell.edu/coffee/</a>).</p><p>Details of the new EST-SSR markers developed using EST database and validated using diverse coffee genotypes in the present study.</p

Details of primer pairs for additional new EST-SSR markers designed in the present study.

<p>*: Unigene ID as per downloaded from the SGN ftp site <a href="ftp://ftp.sgn.cornell.edu/coffee/" target="_blank">ftp://ftp.sgn.cornell.edu/coffee/</a>.</p><p>Details of primer pairs for additional new EST-SSR markers designed in the present study.</p

Map positions of 18 new SSR markers developed in this study (11 CCESSR and 7 CCRM markers) on robusta linkage map; mapping population was derived from a cross between CxR (a commercial robusta hybrid) and a local selection Kagganahalla [26].

<p>The SSR markers of the existing map used as anchor markers are shown in italic and bold face.</p