Honggen Zhang

Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication.

Rice plant architecture is an important agronomic trait and a major determinant in high productivity. Panicle erectness is the preferred plant architecture in japonica rice, but the molecular mechanism underlying domestication of the erect panicle remains elusive. Here we report the map-based cloning of a major quantitative trait locus, qPE9-1, which plays an integral role in regulation of rice plant architecture including panicle erectness. The R6547 qPE9-1 gene encodes a 426-amino-acid protein, homologous to the keratin-associated protein 5-4 family. The gene is composed of three Von Willebrand factor type C domains, one transmembrane domain, and one 4-disulfide-core domain. Phenotypic comparisons of a set of near-isogenic lines and transgenic lines reveal that the functional allele (qPE9-1) results in drooping panicles, and the loss-of-function mutation (qpe9-1) leads to more erect panicles. In addition, the qPE9-1 locus regulates panicle and grain length, grain weight, and consequently grain yield. We propose that the panicle erectness trait resulted from a natural random loss-of-function mutation for the qPE9-1 gene and has subsequently been the target of artificial selection during japonica rice breeding.

CENTRAL REGION COMPONENT1, a Novel Synaptonemal Complex Component, Is Essential for Meiotic Recombination Initiation in Rice

This work identifies CRC1 (for CENTRAL REGION COMPONENT1), a novel synaptonemal complex component that is essential for the initiation of homologous recombination in meiosis. CRC1 is the rice ortholog of budding yeast Pch2 and mouse TRIP13, but the roles of CRC1 identified here have not been reported for Pch2 or TRIP13. In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated CENTRAL REGION COMPONENT1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID RECEPTOR-INTERACTING PROTEIN13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.

A New GA-Insensitive Semidwarf Mutant of Rice (Oryza sativa L.) with a Missense Mutation in the SDG Gene

A semidwarf line of Indica rice, Xinguiai, was derived from the progeny of a cross between the double dwarf mutant Xinguiaishuangai and the wild-type variety Nanjing 6. The semidwarf phenotype was controlled by the semidwarf gene, sdg. The second sheath and shoot elongation responses of the dwarf mutant to exogenous gibberellin (GA3) showed that sdg was insensitive to gibberellin (GA), and its endogenous GAs content was higher than that in wild-type cultivars. The SDG gene was cloned by a map-based cloning method and sequencing analysis revealed that the coding region of sdg had a single nucleotide substitution resulting in a single amino acid change from alanine to threonine. A cleaved amplified polymorphic sequence marker was designed according to sequences from mutant and wild-type materials. This sequence marker could be used to distinguish wild types and mutants, and thus, could be used for molecular marker-assisted selection. The dwarf phenotype of the sdg mutant was restored to a normal phenotype by introducing the wild-type SDG gene. Rice transformation experiments and GUS staining demonstrated that the SDG gene was predominantly expressed in vegetative organs.

Rf5 is able to partially restore fertility to Honglian-type cytoplasmic male sterile japonica rice (Oryza sativa) lines

Three-line japonica hybrids have been developed mainly on Chinsurah Boro II (BT)-type cytoplasmic male sterile (CMS) lines of Oryzasativa L., but the unstable sterility of some BT-type CMS lines, and the threat of genetic vulnerability when using a single cytoplasm source, have inhibited their use in rice cultivation. Previously, the sterility of Honglian (HL)-type japonica CMS lines derived from common red-awned wild rice (Oryzarufipogon) has been proven to be more stable than that of BT-type japonica CMS lines. Here, we genetically characterized HL-type japonica CMS lines and the restorer-of-fertility (Rf) gene for breeding HL-type japonica hybrids. HL-type japonica CMS lines displayed stained abortive pollen grains, unlike HL-type indica CMS lines. The BT-type japonica restorer lines, which contain Rf, had different capabilities to restore HL-LiuqianxinA (HL-LqxA), an HL-type japonica CMS line, and the restorers for the HL-type japonica CMS lines could be selected from the preexisting BT-type japonica restorers in rice production. A genetic analysis showed that the restoration of normal fertility to HL-LqxA was controlled by a major gene and was affected by minor effector genes and/or modifiers. The major Rf in SiR2982, a BT-type japonica restorer, was mapped to a ~100-kb physical region on chromosome 10, and was demonstrated to be Rf5 (Rf1a) by sequencing. Furthermore, Rf5 partially restored fertility and had a dosage effect on HL-type japonica CMS lines. These results will be helpful for the development of HL-type japonica hybrids.

Mapping QTLs conferring resistance to rice black-streaked dwarf disease in rice ( Oryza sativa L)

Rice black-streaked dwarf disease, caused by the rice black-streaked dwarf virus (RBSDV), can lead to severe yield losses in rice. The deployment of resistant cultivars is an effective disease control measure, but few studies related to the genetics and breeding of RBSDV resistance have been reported in rice. Here, we identified ‘IR36’ (indica) and ‘L5494’ (japonica) as resistant and susceptible parents, respectively, using a field test, and 208 recombinant inbred lines were derived from their cross. A genetic analysis indicated that the resistance of rice materials to RBSDV was controlled by quantitative trait loci (QTLs). A total of 12 QTLs for RBSDV resistance on chromosomes 1, 6, 8 and 9 were identified in three environments (2013–2015), and QTLs in two marker intervals, RM19234–CHR6-2 and RM3700–RM160 on chromosomes 6 and 9, respectively, were consistently detected. These QTLs explained 6.19–29.00xa0% of the total phenotypic variation for rice black-streaked dwarf disease incidence. The alleles enhancing resistance on chromosomes 6 and 8 originated from ‘IR36’, whereas the alleles on chromosomes 1 and 9 originated from ‘L5494’. The materials and identified resistance QTLs in this study are expected to be useful resources for efficiently breeding rice cultivars resistant to RBSDV.

Rf4 has minor effects on the fertility restoration of wild abortive-type cytoplasmic male sterile japonica (Oryza sativa) lines

Wild abortive (WA)-type cytoplasmic male sterility (CMS) has been exclusively used for breeding three-line hybrid indica rice, but it has not been applied for generating japonica hybrids because of the difficulties related to breeding japonica restorer lines. Determining whether the major restorer-of-fertility (Rf) gene used for indica hybrids can efficiently restore the fertility of WA-type japonica CMS lines may be useful for breeding WA-type japonica restorer lines. In this study, japonica restorer lines for Chinsurah Boro II (BT)-type CMS exhibited varying abilities to restore the fertility of ‘WA-LiuqianxinA’, which is a WA-type japonica CMS line. Additionally, Rf genes for WA-type CMS were identified in the BT-type japonica restorers. Meanwhile, ‘C9083’, which is a BT-type japonica restorer, exhibited a limited ability to restore the fertility of WA-type japonica CMS lines, and a genetic analysis revealed that the fertility restoration was controlled by one locus. The Rf gene was mapped to an approximately 370-kb physical region and was identified as Rf4. Furthermore, Rf gene dosage effects and the temperature influenced the fertility restoration of WA-type japonica CMS lines. This study is the first to confirm that Rf4 has only minor effects on the fertility restoration of WA-type japonica CMS lines. These results may be relevant for the development of WA-type japonica hybrids.

Improving the Resistance of Wuyunjing 8 to Rice Stripe Virus via Molecular Marker-assisted Selection: Improving the Resistance of Wuyunjing 8 to Rice Stripe Virus via Molecular Marker-assisted Selection

In this study, a molecular marker-assisted selection (MAS) strategy was used to improve Wuyunjing 8s resistance to rice stripe virus. The Wuyunjing 8 with high yield and erect head selected from 25 late-maturing varieties was used as accepter, and the variety Kuifeng with resistance to rice stripe virus as the donor. Four STS (sequence-tagged site) primers STS11-31, STS11-7, STS11-19, and STS11-43 anchoring the resistance genes were used for assisted selection in the backcross progenies. To 2008, seventy lines in BC3F5 and one hundred and fifteen lines of BC4F4 with stable agronomic traits were obtained with the result of molecular analysis. By appraising agronomic traits, yield, quality and resistance in backcross progenies, teen lines from BC4F5 and two lines from BC3F6, which all carried disease-resistant genes and were similar to Wuyunjing 8 on the integrated traits, were selected. These lines retain the characteristics of high yield and good quality of Wuyunjing 8 and have been prominently improved in resistance to rice stripe virus. Keywords: Japonica; Rice stripe virus; Resistance; Improvement; Molecular marker-assisted selection

Improvement of Resistance to Rice Stripe Virus in Wuyunjing 8 via Molecular Marker-Assisted Selection

Abstract A molecular marker-assisted selection (MAS) strategy was used to improve resistance to Rice stripe virus (RSV) in rice (Oryza sativa L. subsp. japonica cv. Wuyunjing 8). Rice variety “Aoikaze” with resistance to RSV was used as the donor. Sequence-tagged site (STS) markers STS11-31, STS11-7, STS11-19, and STS11-43 anchoring the resistance loci were used for MAS in the backcross progenies. In 2008, 70 lines of BC3F5 and 115 lines of BC4F4 population were obtained with stable agronomic traits after MAS assay. Further evaluation of agronomic traits, yield, grain quality, and resistance to RSV were carried out in these backcross progenies, and 10 BC4F5 lines and 2 BC3F6 lines showed similar phenotypes to Wuyunjing 8. The 12 lines were finally selected for the improved resistance to RSV and the high-yield and elite-quality of Wuyunjing 8.