Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling

Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.

Integrated genome-wide association study and QTL mapping reveals qSa-3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

BACKGROUND

The English grain aphid, Sitobion avenae (Fabricius), is a devastating pest impacts yield and quality in wheat (Triticum aestivum L.). Breeding resistant wheat varieties and detecting resistance genes are important strategies to control aphid.

RESULTS

In this study, we evaluated the number of aphids per spike, the rate of thousand kernel weight decrease and aphid index based on three classic resistance mechanisms (antibiosis, tolerance and antixenosis), and detected SNPs/QTLs for resistance to S. avenae in a natural population of 163 varieties with 20 689 high-quality single-nucleotide polymorphism (SNP) markers and recombinant inbred line (RIL) population of 164 lines with 3627 diversity arrays technology (DArT) markers. Results showed that 83 loci significantly associated with S. avenae antibiosis and 182 loci significantly associated with S. avenae tolerance were detected by genome-wide association study (GWAS), explaining 6.47-15.82% and 8.36-35.61% of the phenotypic variances, respectively. The wsnp_Ku_c4568_8243646 detected in two periods was localized at 34.52 Mb on chromosome 3AS. Then, we confirmed a stable QSa.haust-3A.2 explained 11.19-20.10% of the phenotypic variances in two periods with S. avenae antixenosis in the physical interval of 37.49-37.50 Mb on chromosome 3A in the RIL population. Therefore, a narrow region in the physical interval of 34.52-37.50 Mb on chromosome 3AS was named as qSa-3A, which was a new locus between wsnp_Ku_c4568_8243646 and QSa.haust-3A.2 associated with S. avenae resistance.

CONCLUSION

We found qSa-3A was a new locus associated with S. avenae resistance. The results could be applied in gene cloning and genetic improvement of S. avenae resistance in wheat. © 2023 Society of Chemical Industry.

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2-6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5-6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.

The Next Generation of Rice: Inter-Subspecific Indica-Japonica Hybrid Rice

Rice (Oryza sativa) is an important food crop and has two subspecies, indica and japonica. Since the last century, four generations of rice varieties have been applied to rice production. Semi-dwarf rice, intra-subspecific hybrid rice, and inter-subspecific introgression rice were developed successively by genetic modification based on the first generation of tall rice. Each generation of rice has greater yield potential than the previous generation. Due to the stronger heterosis of indica-japonica hybrids, utilization of the inter-subspecific heterosis has long been of interest. However, indica-japonica hybrid sterility hinders the utilization of heterosis. In the past decades, indica-japonica hybrid sterility has been well understood. It is found that indica-japonica hybrid sterility is mainly controlled by six loci, S5, Sa, Sb, Sc, Sd, and Se. The indica-japonica hybrid sterility can be overcome by developing indica-compatible japonica lines (ICJLs) or wide-compatible indica lines (WCILs) using genes at the loci. With the understanding of the genetic and molecular basis of indica-japonica hybrid sterility and the development of molecular breeding technology, the development of indica-japonica hybrid rice has become possible. Recently, great progress has been made in breeding indica-japonica hybrid rice. Therefore, the indica-japonica hybrid rice will be the next generation of rice. It is expected that the indica-japonica hybrid rice will be widely applied in rice production in the near future.