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.

Mapping and Characterization of QTLs for Awn Morphology Using Crosses between “Double-Awn” Wheat 4045 and Awnless Wheat Zhiluowumai

Awns play important roles in seed dispersal, protection against predators, and photosynthesis. The characterization of genes related to the formation of awns helps understand the regulation mechanisms of awn development. In the present study, the “double-awn” wheat 4045, which features super-long lemma awns and long glume awns, and an awnless wheat line, Zhiluowumai, were used to investigate QTLs or genes involved in awn development. QTL analysis identified three loci—Qawn-1D, Qawn-5A, and Qawn-7B—using a population of 101 4045 × ZLWM F2 plants. Fine mapping with a total of 9018 progenies narrowed the mapping interval of Qawn-5A to an 809-kb region, which was consistent with the B1 locus, containing five genes on chromosome 5AL. Gene structure and expression analysis indicated that TraesCS5A02G542800 was the causal gene, which was subsequently verified by overexpression of TraesCS5A02G542800 in a “double-awn” wheat, Yangmai20. The retained “double-awn” phenotype of transgenic plants suggested that B1 represses the elongation but does not influence the emergence of the awns. Moreover, 4045 harbors a new allele of B1 with a 261-bp insertion in the promoter region and a lack of the EAR2 motif in the encoding region, which influences several important agronomic traits. In this study, we identify two novel QTLs and a novel allele of B1, providing new resources for exploration of awn development.

Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel allele candidates (NACs) using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the NACs detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.

Knowledge-based antibody repertoire simulation, a novel allele detection tool evaluation and application

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel alleles using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the novel alleles detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.