Molecular analysis of Oryza latifolia Desv. (CCDD genome)-derived introgression lines and identification of value-added traits for rice (O. sativa L.) improvement

Alien introgression and morpho-agronomic characterization of diploid progenies of Solanum lycopersicoides monosomic alien addition lines (MAALs) toward pre-breeding applications in tomato (S. lycopersicum)

Alien introgressions that were captured in the genome of diploid plants segregating from progenies of monosomic alien addition lines of S. lycopersicoides confer novel phenotypes with commercial and agronomic value in tomato breeding. Solanum lycopersicoides is a wild relative of tomato with a natural adaptation to a wide array of biotic and abiotic challenges. In this study, we identified and characterized diploid plants segregating from the progenies of monosomic alien addition lines (MAALs) of S. lycopersicoides to establish their potential as donors in breeding for target trait improvement in tomato. Molecular genotyping identified 28 of 38 MAAL progenies having the complete chromosome complement of the cultivated tomato parent and limited chromosome introgressions from the wild S. lycopersicoides parent. Analysis of SSR and indel marker profiles identified 34 unique alien introgressions in the 28 MAAL-derived introgression lines (MDILs) in the genetic background of tomato. Conserved patterns of alien introgressions were detected among sibs of MDILs 2, 3, 4 and 8. Across MDILs, a degree of preferential transmission of specific chromosome segments was also observed. Morphologically, the MDILs closely resembled the cultivated tomato more than S. lycopersicoides. The appearance of novel phenotypes in the MDILs that are lacking in the cultivated parent or the source MAALs indicates the capture of novel genetic variation by the diploid introgression lines that can add commercial and agronomic value to tomato. In particular, screening of representative MDILs for drought tolerance at the vegetative stage identified MDIL 2 and MDIL 11III as drought tolerant based on visual scoring. A regulated increase in stomatal conductance of MDIL 2 under drought stress indicates better water use efficiency that allowed it to survive for 7 days under 0% moisture level.

Development of a PCR-based, genetic marker resource for the tomato-like nightshade relative, Solanum lycopersicoides using whole genome sequence analysis

Solanum lycopersicoides is a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilize S. lycopersicoides as a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific to S. lycopersicoides are limited in number, distribution and polymorphism rate. In this study, we developed a suite of S. lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb of S. lycopersicoides contigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci in S. lycopersicoides for which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments between S. lycopersicoides and tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets in S. lycopersicoides and polymorphic loci between S. lycopersicoides and tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource for S. lycopersicoides, as well as for related Solanum spp. for applications in genetics and breeding studies.

A novel locus from the wild allotetraploid rice species Oryza latifolia Desv. confers bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in rice (O. sativa)

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major limiting factor to rice productivity worldwide. Genetic control through the identification of novel sources of bacterial blight resistance and their utilization in resistance breeding remains the most effective and economical strategy to manage the disease. Here we report the identification of a novel locus from the wild Oryza species, Oryza latifolia, conferring a race-specific resistance to Philippine Xoo race 9A (PXO339). The locus was identified from two introgression lines i.e. WH12-2252 and WH12-2256 that segregated from O. latifolia monosomic alien addition lines (MAALs). The discrete segregation ratio of susceptible and resistant phenotypes in the F2 (χ2[3:1] = 0.22 at p>0.05) and F3 (χ2[3:1] = 0.36 at p>0.05) populations indicates that PXO339 resistance in the MAAL-derived introgression lines (MDILs) is controlled by a single, recessive gene. Genotyping of a total of 216 F2, 1130 F3 and 288 F4 plants derived from crossing either of the MDILs with the recurrent parent used to generate the MAALs narrowed the candidate region to a 1,817 kb locus that extends from 10,425 to 12,266 kb in chromosome 12. Putative candidate genes that were identified by data mining and comparative sequence analysis can provide targets for further studies on mapping and cloning of the causal gene for PXO339 resistance in the MDILs. To our knowledge, this is the first report of a genetic locus from the allotetraploid wild rice, O. latifolia conferring race-specific resistance to bacterial blight.

Production and cytological characterization of a synthetic amphiploid derived from a cross between Oryza sativa and Oryza punctata

Oryza punctata Kotschy ex Steud. (BB, 2n = 24) is a wild species of rice that has many useful agronomic traits. An interspecific hybrid (AB, 2n = 24) was produced by crossing O. punctata and Oryza sativa variety Punjab Rice 122 (PR122, AA, 2n = 24) to broaden the narrow genetic base of cultivated rice. Cytological analysis of the pollen mother cells (PMCs) of the interspecific hybrids confirmed that they have 24 chromosomes. The F₁ hybrids showed the presence of 19-20 univalents and 1-3 bivalents. The interspecific hybrid was treated with colchicine to produce a synthetic amphiploid (AABB, 2n = 48). Pollen fertility of the synthetic amphiploid was found to be greater than 50% and partial seed set was observed. Chromosome numbers in the PMCs of the synthetic amphiploid were 24II, showing normal pairing. Flow cytometric analysis also confirmed doubled genomic content in the synthetic amphiploid. Leaf morphological and anatomical studies of the synthetic amphiploid showed higher chlorophyll content and enlarged bundle sheath cells as compared with both of its parents. The synthetic amphiploid was backcrossed with PR122 to develop a series of addition and substitution lines for the transfer of useful genes from O. punctata with least linkage drag.

Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application

Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F₁, and the F₁ plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC₁F₁ and 73 BC₂F₁ plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F₁, BC₁F₁, BC₂F₂, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.

Development of an intergeneric hybrid between Oryza sativa L. and Leersia perrieri (A. Camus) Launert

An intergeneric hybrid was successfully developed between Oryza sativa L. (IRRI 154) and Leersia perrieri (A. Camus) Launert using embryo rescue technique in this study. A low crossability value (0.07%) implied that there was high incompatibility between the two species of the hybrid. The F1 hybrid showed intermediate phenotypic characteristics between the parents but the plant height was very short. The erect plant type resembled the female parent IRRI 154 but the leaves were similar to L. perrieri. Cytological analysis revealed highly non-homology between chromosomes of the two species as the F1 plants showed 24 univalents without any chromosome pairing. The F1 hybrid plant was further confirmed by PCR analysis using the newly designed 11 indel markers showing polymorphism between O. sativa and L. perrieri. This intergeneric hybrid will open up opportunities to transfer novel valuable traits from L. perrieri into cultivated rice.

Development of Oryza sativa L. by Oryza punctata Kotschy ex Steud. monosomic addition lines with high value traits by interspecific hybridization

This paper describes the development of monosomic alien addition and disomic introgression lines through a cross between autotetraploid indica rice and Oryza punctata toward tapping valuable traits for rice improvement. Oryza punctata is a distantly related wild Oryza species having BB genome with untapped genetic resources for rice improvement. Low crossability between the cultivated O. sativa and O. punctata restricts the success of transferring many desirable traits into cultivated rice. Artificially induced autotetraploids of an elite breeding line, IR31917-45-3-2, were produced and crossed with O. punctata. Allotriploid F1 plants were backcrossed to IR31917-45-3-2 and generated progenies with extra chromosomes from O. punctata. Twenty BC1F1 and 59 BC2F1 plants were produced with chromosome numbers ranging from 24 (2n) to 29 (2n + 5) and 2n (24) to 26 (2n + 2), respectively. Eleven monosomic alien addition lines (MAALs) were characterized morphologically and cytologically and designated as MAAL 1-12. MAALs were genotyped using O. punctata genome-specific molecular markers and detected chromosome segments inherited from O. punctata. O. punctata introgressions across all the chromosomes of O. sativa were identified except for chromosome 8. The most frequent introgressions were observed in chromosomes 4, 6, 10, and 11, which could be the recombination hotspots between A and B genomes. Some of the qualitative traits such as black hull, purple coleoptile base, purple stigma, long awn, and short grain size from O. punctata were inherited in some disomic introgression lines (DILs). Several DILs inherited genes from O. punctata conferring resistance to brown planthopper, green leafhopper, and diseases such as bacterial blight and blast. This is the first report on successful gene transfer from O. punctata into O. sativa.

Phenotypic and Marker-Assisted Genetic Enhancement of Parental Lines of Rajalaxmi, an Elite Rice Hybrid

The cytoplasmic male sterile line system comprising CRMS 32A and its maintainer line CRMS 32B is a popular choice for the development of new hybrids in India as CRMS 32A, having Kalinga 1 cytoplasm (other than WA), is a viable alternative to WA cytoplasm. However, both lines are susceptible to bacterial blight (BB), a major disease on rice. As enhancement of host plant resistance is the most effective and economical strategy to control this disease, four resistance genes (Xa4, xa5, xa13, and Xa21) were transferred from a BB pyramid line of IR64, into the A and B lines using a marker-assisted backcrossing (MAB) breeding strategy. During the transfer of genes into CRMS 32B, foreground selection was applied using markers associated with the genes, and plants having resistance alleles of the donor, are selected. Selection for morphological and quality traits was practiced to select plants similar to the recurrent parent. The four gene and three gene pyramid lines exhibited high levels of resistance against the BB pathogen when challenged with eight virulent isolates. Using genome wide based SSR markers for background selection, pyramids having >95% of the recurrent parent genome were identified. With CRMS 32B gene pyramid as donor, the four resistance genes were transferred into the A line through repeated backcrosses and the A line pyramids also exhibited high level of resistance against BB. Through a combination of selection at phenotypic and molecular levels, four BB resistance genes were successfully introduced into two parental lines (CRMS 32 B and A) of Rajalaxmi, an elite popular hybrid. The pyramided B lines did exhibit high levels of resistance against BB. Selection for morphological and quality traits and background selection hastened the recovery of the recurrent parent genome in the recombinants. Through repeated backcrosses, all the four resistance genes were transferred to CRMS 32A and test crosses suggest that the maintenance ability of the improved CRMS 32B lines is intact. These improved maintainer and CMS lines can directly be used in hybrid rice breeding and the new hybrids can play an important role in sustainable rice production in India.

Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha

African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.