Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q?+?K) model using GAPIT software. At p-value?<?0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

     

Effectiveness of crop protection methods against wildlife damage: A case study of two villages at Bardia National Park,Nepal

Conflicts due to damage caused by wildlife pose serious threats to conservation. In addition, wildlife damage incurs severe economic loss to communities living in the close vicinity of the park, affecting the livelihoods and well-being of locals. While different studies have emphasised identification and quantification of crop damage problems, studies highlighting the means used for crop protection and their effectiveness are limited. This study aimed to examine the effectiveness of means used by communities to protect their crops against wildlife. 117 households were visited at two Buffer Zone villages of Bardia National Park, Nepal. Findings suggested that crop depredation by wildlife was a function of several factors, such as the distance of the farmland from the park, the size of the crop raiding animals and the frequency of attacks on the farmland, and the type of crops. Ten different means were identified by communities which were used regularly to prevent crop damage. Households combined both traditional and modern means to guard their crop against the wild animals. Means differed according to the animals as well as crops being protected. Among all these means, Machan (i.e. watch towers) combined with other means such as throwing flaming sticks and group shouting were the most effective and safest modes of crop guarding for all kinds of animals and crops. Trench and Bio-fencing were effective mostly for deer species. However, crop guarding was an intensive process and no means were able to completely prevent crop damage. Problem animals differed according to the villages and crops being damaged, which suggests that employment of single means would be ineffective. Site-specific management strategies and economic as well as technical support from funding organisations would be most useful to minimise crop loss. In addition information exchange and learning between farmers and the park management about different mitigating means could support and prepare farmers for improvement in the means.     

Development of an in vitro protocol to screen Clavibacter michiganensis subsp. michiganensis pathogenicity in different Solanum species

Clavibacter michiganensis subsp. michiganensis (Cmm) is a quarantine organism in Europe and in many other countries. It is one of the most severe bacterial pathogens affecting tomato. Screening tomato plants for their resistance level to Cmm requires a large amount of space under quarantine conditions and is therefore costly. This project developed a new inoculation protocol on in vitro tomato plants to facilitate a more economic and higher throughput disease screening. A new method using the PathoScreen system was tested to localize green fluorescent protein-tagged Cmm in planta and to quantify the pathogen based on the percentage of corrected GFP (cGFP%). The system was sensitive in detecting the GFP-tagged Cmm in the shoots, but in the roots a high autofluorescence masked detection and thus sensitivity of the assay. The in vitro protocol was tested on several wild relatives of tomato, which were previously screened in a greenhouse assay. The correlation between wilt symptoms in vitro and wilt symptoms in the greenhouse was overall moderate (r = 0.6462). The protocol worked well in differentiating the two parents that were used in the mapping studies. This study shows that the in vitro protocol can be efficiently used for resistance breeding in many tomato genotypes.     

Modification of growth and yield responses of Amaranthus tricolor L. to sUV-B under varying mineral nutrient supply

The decrease in stratospheric ozone has heightened concern over the consequences of increasing solar UV-B radiation on plants. The present study was conducted to evaluate the interactive effects of supplemental UV-B (sUV-B: 280–320 nm) and mineral nutrients on a leafy vegetable amaranthus (Amaranthus tricolor L. var Pusa badi) under natural field conditions in a dry tropical environment. The nutrient treatments were recommended dose of NPK, 1.5 times recommended dose of NPK, 1.5 times recommended dose of N and 1.5 times recommended dose of K sUV-B radiation inhibited growth and biomass accumulation and altered the patterns of biomass partitioning. In K amended plants larger proportion of biomass has been translocated to roots which further increased under sUV-B treatment. The application of 1.5 times recommended dose of NPK reduced the magnitude of yield loss. The study shows that amaranthus is a potentially UV-B sensitive species and a higher NPK dose above the recommended is required to minimize the adverse impact of sUV-B.     

Conservation and climate change: Assessing the vulnerability of snow leopard habitat to treeline shift in the Himalaya

Climate change is likely to affect the persistence of large, space-requiring species through habitat shifts, loss, and fragmentation. Anthropogenic land and resource use changes related to climate change can also impact the survival of wildlife. Thus, climate change has to be integrated into biodiversity conservation plans. We developed a hybrid approach to climate-adaptive conservation landscape planning for snow leopards in the Himalayan Mountains. We first mapped current snow leopard habitat using a mechanistic approach that incorporated field-based data, and then combined it with a climate impact model using a correlative approach. For the latter, we used statistical methods to test hypotheses about climatic drivers of treeline in the Himalaya and its potential response to climate change under three IPCC greenhouse gas emissions scenarios. We then assessed how change in treeline might affect the distribution of snow leopard habitat. Results indicate that about 30% of snow leopard habitat in the Himalaya may be lost due to a shifting treeline and consequent shrinking of the alpine zone, mostly along the southern edge of the range and in river valleys. But, a considerable amount of snow leopard habitat and linkages are likely to remain resilient to climate change, and these should be secured. This is because, as the area of snow leopard habitat fragments and shrinks, threats such as livestock grazing, retaliatory killing, and medicinal plant collection can intensify. We propose this approach for landscape conservation planning for other species with extensive spatial requirements that can also be umbrella species for overall biodiversity.     

Where have all the sawfishes gone? Perspectives on declines of these Critically Endangered species in Sri Lanka

1. All five species of sawfishes (family Pristidae) are amongst the most threatened marine fishes in the world, with steep population declines and local extinctions documented across their ranges.
2. Sawfishes have featured in Sri Lankan species checklists since 1889. However, landing records are extremely rare and little information is available on their status, diversity, and recent occurrences.
3. Interviews were conducted with 300 fishers and 10 fish traders. Only 39% of fishers (n = 118) could identify sawfishes, 37% had seen sawfishes (although half not since 1992), and only 10.7% had ever caught one. No respondents under 30 years could identify sawfishes. Older respondents (>50 years) were more likely to have caught sawfishes and reported seeing them frequently until 30 years ago, while younger respondents had only seen them at landing sites and, at most, once or twice in their life. Only 10 respondents had seen a sawfish in the last decade, suggesting that sawfishes were relatively abundant in the past but that populations have drastically declined.
4. Of the 32 respondents who had caught sawfishes, 30 reported declining numbers and attributed it to fishing pressure. These steep declines coincide with the time of increased fishing effort, the development of the aquaculture industry, and resulting degradation of coastal habitats in the 1980–1990s.
5. Overall, sawfishes had little cultural significance although fishers had specific names for the different species occurring here and rostra were sometimes donated to Catholic churches for ‘good luck’. Landed sawfishes were primarily sold for meat and traders appeared unaware of the high value of fins.
6. It is likely that sawfishes are now functionally extinct as a component of coastal ecosystems in Sri Lanka. Immediate action including species-specific legislation and critical habitat protection is urgently needed to provide remaining sawfishes and other sharks and rays with a fighting chance.