Hybrid rice development, a major advance in rice breeding, has demonstrated its immense potential in enhancing the rice productivity. In the three line system of hybrid rice, the restoration of fertility of the widely used wild-abortive type of cytoplasmic male sterility is controlled by Rf3 and Rf4, two fertility restoration genes. Exploration for restorers in diverse genetic backgrounds is a critical step in hybrid rice breeding. As genetic resources constitute the major source of new genes/alleles, an attempt was made to assess the distribution of these two restorer genes in the native populations collected from the geographic regions known to be the primary and secondary centres of origin of rice. In addition, assays were performed on the populations of Oryza rufipogon and Oryza nivara, the wild progenitors of rice. The results suggest that the Rf genes are well distributed in the wild forms at a higher frequency, more in O. rufipogon, while in cultivated forms, their frequency is low, particularly for the Rf3 gene. The genes and the alleles identified in the genetically divergent, low-performing land races and wild relatives can be successfully employed for the development of new hybrid rice cultivars.

In this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

The goal of most rice improvement programs is the enhancement of farmers’ yield using less land and limited water. This study evaluated 77 upland rice genotypes under optimal upland growing conditions in the field and ranked the genotypes using base indices. Subsequently, eighteen cultivars selected from the field trial were screened under drought in rainout-shelter conditions. The traits evaluated for index selection were yield, days to flowering, plant height, number of panicles and filled grains. Under field conditions, based on the sum of economic weight assigned to five traits used to compute the selection index, IR 68704-145-1-1-B and IR 63380-16 were the best genotypes. In the rainout-shelter experiment, Ofada 2 (508 gm−2) had the highest grain yield under non-stress conditions while ITA 117 (152.38 gm−2) had the highest grain yield under drought stress. The base index was efficient for selecting superior genotypes with the best combination for all the traits considered. Susceptibility to drought stress of the landraces leads to poor grain yield.

We developed novel and polymorphic microsatellite primers for Spathoglottis plicata, a tropical and subtropical terrestrial orchid, to investigate the genetic patterns and population structure among wild populations, and also to identify the varieties and hybrids of S. plicata in horticultural industry. The 12 novel microsatellites from S. plicata were developed by using polymerase chain reaction (PCR)-based isolation of microsatellite arrays. These markers that were successfully PCR amplified exhibited polymorphisms in S. plicata. The number of alleles, observed heterozygosity, expected heterozygosity and polymorphism information content values across loci ranged from 2.000 to 8.000, 0.000 to 0.756, 0.208 to 0.813 and 0.405 to 0.805 in total populations, respectively. The newly developed microsatellite markers exhibited variation in S. plicata. These markers can be used as a tool to further investigate the genetic diversity, conservation genetics and variety/hybrid identification of S. plicata.

Galantamine (GAL), a morphine-like alkaloid produced by some members of the Amaryllidaceae plant family, is a possible therapeutic agent in Alzheimer's disease because of its central cholinergic effects. GAL has been extracted from the plant sources or produced synthetically for pharmaceutical use. Limited supply of the natural source and high cost of synthetic production has led to a search for alternative sources of this valuable compound. In the present study, a total of six Galanthus nivalis populations (GNPs) and 11 Narcissus tazetta populations (NTPs) were collected across different regions of Iran and were then subjected to the high-performance liquid chromatography analysis for their GAL quantification. The GAL content ranged from 0.05 to 0.36 mg/g dry weight (DW) in the bulbs of GNPs, and from 0.03 to 0.33 mg/g DW in the bulbs of NTPs. Maximum content of GAL (0.36 and 0.33 mg/g DW) was measured in the Zirab population of G. nivalis and Ghaemshahr population of N. tazetta, respectively. Our results provided a suitable material for further agronomical and biotechnological strategies for enhanced production of valuable GAL compound on a large scale.

Dongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

The red algal genus Porphyra is sister to the genus Pyropia, the single most valuable marine crop in the Orient. We developed microsatellite loci for the red alga Porphyra umbilicalis, a widespread species in the Northern Atlantic. Enriched DNA libraries were constructed and 68 loci were screened for amplification and polymorphism. Seven polymorphic microsatellite markers were isolated using 44 individuals collected from four natural populations. The number of alleles per locus ranged from two to 12. Null alleles were detected in three loci. Among the markers reported, we tested also cross-amplification with two other Porphyra spp. These polymorphic microsatellite markers should be useful for investigating population genetic structure of P. umbilicalis in the North East Atlantic.

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Pearl millet is an important cereal crop for smallholder farmers’ food security in Africa and India. However, its production has stagnated due to several factors such as downy mildew (DM). Thus, a study was conducted to identify new sources of resistance from pearl millet inbred lines derived from a collection of landraces originated from West and Central African countries. A set of 101 lines, including 99 inbred lines from West and Central Africa along with a 7042S and SOSAT C 88 as susceptible and resistant checks, respectively, were evaluated under field conditions with infector rows in Bambey and Nioro research stations during the rainy season of 2016. Data on DM incidence and severity, plant height, flowering time, panicle length and productive tillers were recorded. The results showed highly significant differences among lines for all observed traits. Among the tested lines, 55 including SOSAT C 88 were resistant, 16 moderately resistant and 30 including 7042S were susceptible to the disease. Out of the 55 resistant lines, 20 were disease free. Hierarchical ascendant cluster analysis grouped the lines into three clusters with the DM parameters and plant height as the most discriminant factors. Cluster II contains the susceptible lines, while cluster III comprises the moderately resistant lines. The lines which belongs to cluster I were characterized by their resistance to the disease. Further use of these available new sources of resistance will be very useful for improvement of pearl millet for DM resistance and other agronomic traits.