Interaction between photoperiod and variation in circadian rhythms in tomato

Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust to the time of the year. Modification of circadian clocks is especially relevant in crops to enhance their cultivability in specific regions by changing their sensibility to photoperiod. In tomato, the appearance of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) during domestication delayed its circadian rhythms, and allowed its expansion outside its equatorial origin. Here we study how variation in circadian rhythms in tomato affects its perception of photoperiod. To do this, we create near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and perform transcriptomic profiling under two different photoperiods. We observe that EID1, but not LNK2, has a large effect on the tomato transcriptome and its response to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms.

Drought Tolerant Near Isogenic Lines of Pusa 44 Pyramided With qDTY2.1 and qDTY3.1, Show Accelerated Recovery Response in a High Throughput Phenomics Based Phenotyping

Reproductive stage drought stress (RSDS) is a major challenge in rice production worldwide. Cultivar development with drought tolerance has been slow due to the lack of precise high throughput phenotyping tools to quantify drought stress-induced effects. Most of the available techniques are based on destructive sampling and do not assess the progress of the plant’s response to drought. In this study, we have used state-of-the-art image-based phenotyping in a phenomics platform that offers a controlled environment, non-invasive phenotyping, high accuracy, speed, and continuity. In rice, several quantitative trait loci (QTLs) which govern grain yield under drought determine RSDS tolerance. Among these, qDTY2.1 and qDTY3.1 were used for marker-assisted breeding. A set of 35 near-isogenic lines (NILs), introgressed with these QTLs in the popular variety, Pusa 44 were used to assess the efficiency of image-based phenotyping for RSDS tolerance. NILs offered the most reliable contrast since they differed from Pusa 44 only for the QTLs. Four traits, namely, the projected shoot area (PSA), water use (WU), transpiration rate (TR), and red-green-blue (RGB) and near-infrared (NIR) values were used. Differential temporal responses could be seen under drought, but not under unstressed conditions. NILs showed significant level of RSDS tolerance as compared to Pusa 44. Among the traits, PSA showed strong association with yield (80%) as well as with two drought tolerances indices, stress susceptibility index (SSI) and tolerance index (TOL), establishing its ability in identifying the best drought tolerant NILs. The results revealed that the introgression of QTLs helped minimize the mean WU per unit of biomass per day, suggesting the potential role of these QTLs in improving WU-efficiency (WUE). We identified 11 NILs based on phenomics traits as well as performance under imposed drought in the field. The study emphasizes the use of phenomics traits as selection criteria for RSDS tolerance at an early stage, and is the first report of using phenomics parameters in RSDS selection in rice.

Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

The Physicochemical Properties of Starch Are Affected by Wxlv in Indica Rice

Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(Wxlv), NIL(Wxa), and NIL(Wxb) in the indica rice Q11 background containing different Wx alleles. Q11(Wxlv) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying Wxa and Wxb. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(Wxlv) rice. Chain length distribution analysis showed that Q11(Wxlv) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(Wxa) and NIL(Wxb) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of Wxlv on rice grain quality and the fine structure of starch in indica rice.

Comparison of photosynthetic activity and heat tolerance between near isogenic lines of wheat with different photosynthetic rates

Wheat (Triticum aestivum L.) is one of the most important crops in the world, but the yield and quality of wheat are highly susceptible to heat stress, especially during the grain-filling stage. Therefore, it is crucial to select high-yield and high-temperature-resistant varieties for food cultivation. There is a positive correlation between the yield and photosynthetic rate of wheat during the entire grain-filling stage, but few studies have shown that lines with high photosynthetic rates can maintain higher thermotolerance at the same time. In this study, two pairs of wheat near isogenic lines (NILs) with different photosynthetic rates were used for all experiments. Our results indicated that under heat stress, lines with a high photosynthetic rate could maintain the activities of photosystem II (PSII) and key Calvin cycle enzymes in addition to their higher photosynthetic rates. The protein levels of D1 and HSP70 were significantly increased in the highly photosynthetic lines, which contributed to maintaining high photosynthetic rates and ensuring the stability of the Calvin cycle under heat stress. Furthermore, we found that lines with a high photosynthetic rate could maintain high antioxidant enzyme activity to scavenge reactive oxygen species (ROS) and reduce ROS accumulation better than lines with a low photosynthetic rate under high-temperature stress. These findings suggest that lines with high photosynthetic rates can maintain a higher photosynthetic rate despite heat stress and are more thermotolerant than lines with low photosynthetic rates.

Does the Inclusion of Second Generation Genetically Modified Plants in Feeds have any effect on Animal Performance?

The need for studies on the nutritional value of plants depends on their composition. The first generation genetically modified Plants (GMPs) have the same composition as their near-isogenic lines. Therefore, they have the same nutritional value, and most of the animal feeding studies have found no significant differences in the production and health parameters of animals that consumed first-generation GMPs in comparison to non-GMPs. Due to the recent production of transgenic plants with specific nutritional properties (second generation GMPs), their use as feed for animals is viewed with skepticism in very many countries. In this critical review, it is concluded that most of these nutritionally improved plants have not shown adverse effects on the performance of various animals compared to their near-isogenic lines and can therefore be considered in the animal feed industry. However, most of the experiments were conducted on laboratory animals. There is a need to conduct them with animals that are mainly consumed by humans, such as ruminants. There is also a need to feed the whole plant to these animals and not just certain parts of the plant to get a clear picture of its overall safety. In addition, there is a need to determine a suitable long-term nutritional and toxicological approach assessment.

Assessment of potentiality of known bacterial blight resistant genes against Xanthomonas oryzae pv. oryzae pathotypes exist in Bangladesh

Bacterial blight (BB) caused by X. oryzae pv. oryzae is a destructive disease of rice and causes 30-50% losses to rice depending on the outbreak. Development BB resistant rice varieties have long been considered as one of the most effective approach to control the disease. However, the durability of host resistance is breaking down due to the change of pathotypes of X. oryzae pv. oryzae globally. Pathotypic analyses of 239 X. oryzae pv. oryzae Bangladeshi isolates on Near Isogenic Lines (NILs) containing resistance (R) gene (s) revealed the existence of eight pathotypes of X. oryzae pv. oryzae. Among eight pathotypes, pathotypes IV and V were considered as major comprising maximum number of isolates, (30.13% and 23.01%, respectively), whereas pathotype VIII considered as minor consisting only 2.51% of total isolates. Pathotype, I showed highest virulence or aggressiveness compatible with all NILs, whereas pathotype VIII exhibited lowest virulence to these NILs. Bacterial blight resistant genes viz. Xa1 (75.00%), Xa11 (62.50%) and Xa21 (50.00%) showed resistance to most of the pathotypes while Xa4 performed worst as compared to all others R-genes. In pyramid lines, IRBBB63 (Xa5+Xa7+Xa13) and IRBB57 (Xa5+Xa7 +Xa21) showed resistance reaction and IRBB61 (Xa4+Xa5+Xa7), IRBB60 (Xa4+Xa5+Xa13+Xa21), IRBB54 (Xa5+Xa21), and IRBB53 (Xa4+Xa21) showed susceptible reaction to X. oryzae pv. oryzae pathotypes. These results collectively indicated the deployment of Xa1, Xa11, Xa4, Xa5, Xa7, Xa13 and Xa21 either alone or in combination against BB would be a best choice for the development of BB resistant rice varieties in Bangladesh.

Characterisation of a 4A QTL for Metribuzin Resistance in Wheat by Developing Near-Isogenic Lines

Wheat (Triticum aestivum L.) production is constantly affected by weeds in the farming system. Chemical-based weed management is widely practiced; broad-spectrum herbicides such as metribuzin have been successfully used to control weeds in Australia and elsewhere of the world. Breeding metribuzin-resistant wheat through genetic improvement is needed for effective control of weeds. Quantitative trait loci (QTLs) mapping efforts identified a major QTL on wheat chromosome 4A, explaining up to 20% of the phenotypic variance for metribuzin resistance. The quantitative nature of inheritance of this QTL signifies the importance of near-isogenic lines (NILs), which can convert a quantitative trait into a Mendelian factor for better resolution of the QTL. In the current study, NILs were developed using a heterogeneous inbred family method combined with a fast generation-cycling system in a population of Chuan Mai 25 (resistant) and Ritchie (susceptible). Seven pairs of NILs targeting the 4A QTL for metribuzin resistance were confirmed with a molecular marker and phenotyping. The resistant allele from the resistant parent increased metribuzin resistance by 63–85% (average 69%) compared with the susceptible allele from the susceptible parent. Segregation analysis in the NIL pairs for thousand grain weight (TGW) (g), biomass per plant (kg), tillers per plant, plant height (cm), yield per plant, and powdery mildew visual score (0–9) indicated that these traits were linked with metribuzin resistance. Similarly, TGW was observed to co-segregate with metribuzin resistance in most confirmed NILs, signifying that the two traits are controlled by closely linked genes. The most contrasting NILs can be further characterised by transcriptomic and proteomic analyses to identify the candidate genes responsible for metribuzin resistance.