Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap

Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population which consists of 1495 samples and wild rice population with 446 samples. Four high coverage sequence hybrid rice accessions and two high coverage sequence wild rice accessions, which were also included in low coverage sequence data, are used to validate the genotype inference accuracy. The validation results showed that HetMap archived significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with other similar software packages. The application of the new genotype with the genome wide association study also showed improvement of association power in two wild rice phenotypes. It could archive high genotype inference accuracy with low sequence coverage with a small population size with both the natural population and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help the discover of new phenotype regions for the plant species with complex heterozygous genome.

Pengaruh pemupukan N terhadap serapan dan efisiensi penggunaan N, serta hasil padi hibrida

Pemupukan N pada padi hibrida menjadi krusial mengingat varietas padi hibrida sangat responsif, sehingga harus diketahui dosis yang tepat untuk menghasilkan produksi yang tinggi. Penelitian ini bertujuan untuk mengkaji pengaruh dosis N terhadap serapan N, efisiensi penggunaan N, dan hasil padi hibrida. Penelitian menggunakan Rancangan Acak Kelompok yang diulang tiga kali. Faktor pertama adalah varietas padi hibrida yang terdiri dari Varietas Mapan P05, Varietas SL-8 SHS Sterling, dan Varietas Intani 602. Faktor kedua adalah dosis pemupukan N yang terdiri dari kontrol tanpa pemupukan N, dosis N 100 kg ha-1, dan dosis N 200 kg ha-1. Terdapat respon yang beragam antar varietas padi hibrida terhadap taraf pemupukan N, Serapan N, efisiensi penggunaan N tertinggi yang dihasilkan oleh varietas Intani 602 masing-masing sebesar 138,57 %, dan 36,13%. Serapan N tanaman padi tertinggi dicapai pada dosis N 100 kg ha-1, dan efisiensi penggunaan N tertinggi pada dosis N 200 kg ha-1. Hasil gabah tertinggi dicapai pada varietas Mapan P05 sebesar 7,42 t ha-1, dan dosis pemupukan N 100 kg ha-1 memberikan hasil tertinggi sebesar 7,47 t ha-1. Implikasi dari penelitian ini bahwa dosis nitrogen 100 kg ha-1 dapat menjadi acuan sebagai dosis pemupukan N varietas padi hibrida di Indonesia. Hybrid rice is responsive to nitrogen, so it’s necessary to find the optimum dose to optimize the production. The aim of this research was to examine the effect of nitrogen on N uptake, N use efficiency, and yield of hybrid rice. This study used a randomized block design with three replications. The first factor consisted of the Mapan P05 variety, the SL-8 SHS Sterling variety, and Intani 602 variety. The second factor was Nitrogen dosage consisted of control, 100 kg ha-1, and 200 kg ha-1. There were various responses among hybrid rice varieties to the level of fertilization. The highest N uptake and N use efficiency was achieved in the Intani 602 variety at 138.57% and 36.13%, respectively. The highest N uptake was achieved at 100 kg ha-1 of N, and the highest N use efficiency was at 200 kg ha-1. The highest yield was achieved in the Mapan P05 variety (7.42 t ha-1), and the dose of N at 100 kg ha-1 gave the highest yield (7.47 t ha-1). The implication of this research is that the nitrogen dose of 100 kg ha-1 can be used as a reference for hybrid rice varieties fertilizer in Indonesia.

PARAMETER OPTIMIZATION AND EXPERIMENT OF SLIDER-HOLE-WHEEL SEED-METERING DEVICE BASED ON DISCRETE ELEMENT METHOD

To improve the adaptability and precision of the slider-hole-wheel seed-metering device to meet the requirements of precision sowing, the single factor simulation experiments and the three factors three levels of orthogonal simulation experiments were carried out based on the discrete element method. The rotation speed of the seeding shaft, the shape of the hole, and the depth of the hole were set as experiment factors. The results of simulation experiments showed that the qualified rate was the highest when the rotation speed of the seeding shaft was 30 r/min, the shape of the hole was oval, and the depth of the hole was 9 mm. The qualified rate, replay rate, and miss-seeding rate were 89.09 %, 3.64 %, and 7.27 %，respectively. The hybrid rice seeds of Zhongnong 2008, Chuangliangyou 4418, and Gangyou 898 were chosen as the materials for the bench and field seeding performance tests to verify the reliability of the simulation results. The test results showed that the qualified rate of Zhongnong 2008, Chuangliangyou 4418, and Gangyou 898 seed in bench tests were 85.07 %, 85.20 %, and 82.13 %, and the qualified rate of Zhongnong 2008, Chuangliangyou 4418, and Gangyou 898 seed in field tests were 82.13 %, 82.27 %, and 80.53 %. The seeding performance with the three kinds of rice seeds could meet the agronomic requirements for precision sowing of hybrid rice. The paper provided the basis for the structure optimization and seeding performance improvement of the slider-hole-wheel seed-metering device.

Genetic Stability of TGMS Hybrids in Dry Direct Seeded Rice

Rice is a water-loving crop and traditionally sown in the nursery and then transplanted to the puddled and waterlogged main field. Owing to climate change, water scarcity and labour shortage problems, rice is now cultivated in the dry direct seeded method. Owing to potential of hybrid rice in increasing both rice production and productivity, many countries are focusing on exploiting the benefits of this technology. To break the yield plateau in rice cultivation, Thermosensitive Genetic Male Sterile (TGMS) hybrids were found to be very effective. In the present study, 41 TGMS hybrids and 9 checks were evaluated for their stability and adaptability by dry direct seeded method in four locations viz., E1 - Allahabad, E2 - Lucknow, E3 - Dhamtari and E4 - Raipur. The TGMS hybrid G44 was predicted as an ideal hybrid by the GGE stability model that possessed high grain yield and stable performance over environments. It was followed by hybrids viz., G10, G14, G34, G11, G20 and G47 that had a stable performance with high yield. Hence, these TGMS hybrids were identified as high and stable yielders across environments and suitable for dry direct seeded rice ecosystems. Among the environments, E1 (Allahabad) and E4 (Raipur) were considered favourable environments as they possessed the highest discriminating power. The hybrids identified in the study can be utilized for breaking the yield barriers in rice and can be recommended for dry direct seeding in marginal and rainfed areas.

QTL Analysis Based on A Rice Short-Wide Grain CSSL-Z414 and Substitution Mapping of qGL11 and qGW5

Background: Most of rice agronomic traits as grain length etc. are complex traits controlled by multiple genes. Chromosome segment substitution lines (CSSLs) are ideal materials for dissecting and studying of these complex traits. Results: We developed a novel rice short-wide grain CSSL, Z414, deriving from progeny of the recipient parent Xihui 18 (an indica restorer line) and the donor parent Huhan 3 (a japonica cultivar). Z414 contained 4 substitution segments (average length was 3.04 Mb). Compared with Xihui 18, Z414 displayed seven significantly different traits as grain length, width and weight, chalkiness degree, brown rice rate etc. Then, 8 quantitative trait loci (QTLs) were found responding these difference traits by F2 population from Xihui 18/Z414. Among them, 6 QTLs (qPL3, qGW5, qGL11, qRLW5, qRLW11, qGWT5) could be verified by novel developed single segment substitution lines (SSSLs, S1-S6). In addition, 4 QTLs (qGL3, qGL5, qCD3 and qCD5) were novel detected by S1 and S5. Thus, the short–wide grain of Z414 was responded by qGL11, qGL3, qGL5, and qGW5. Then, qGL11 and qGW5 were delimited within intervals of 0.405 and 1.14 Mb on chromosomes 11 and 5, respectively, by substitution mapping. Again by sequencing, qRT-PCR and cell morphology analysis, qGW5 should be a novel allele of GS5 and qGL11 is novel QTL encoding CycT1;3, whose specific function of regulating grain length was still unknown. Finally, pyramid of qGL3 (a=0.22) and qGL11 (a=-0.19) displayed qGL11 epistatic to qGL3. In addition, novel S1 and D2 exhibited different grain sizes and lower chalkiness degree. They are potential to be directly used in breeding hybrid rice varieties.Conclusions: We constructed a novel rice short–wide grain CSSL-Z414 with 4 substitution segments based on the genetic backgrounds of Xihui 18. The broad grain of Z414 was controlled by qGW5, which should be a novel allele of GS5. The short grain of Z414 was controlled by qGL11, qGL3, and qGL5, and qGL11 is a novel QTL encoding CycT1;3, whose specific function of regulating grain length was still unknown, and qGL11 is epistatic to qGL3. Novel S1 and D2 are potential in hybrid rice varieties.