While rhizome formation is intimately associated with perennialism and the derived benefit of sustainability, the introduction of this trait into temperate-zone adapted Sorghum cultivars requires precise knowledge of the genetics conditioning this trait in order to minimize the risk of weediness (e.g., Johnsongrass, S. halepense) while maximizing the productivity of perennial sorghum. As an incremental step towards dissecting the genetics of perennialism, a segregating F4 heterogeneous inbred family derived from a cross between S. bicolor and S. propinquum was phenotyped in both field and greenhouse environments for traits related to over-wintering and rhizome formation. An unseasonably cold winter in 2011 provided high selection pressure, and hence 74.8 % of the population did not survive. This severe selection pressure for cold tolerance allowed the resolution of two previously unidentified over-wintering quantitative trait locus (QTL) and more powerful correlation models than previously reported. Conflicting with previous reports, a maximum of 33 % of over-wintering variation could be explained by above-ground shoot formation from rhizomes; however, every over-wintering plant exhibited rhizome growth. Thus, while rhizome formation is required for over-wintering, other factors also determine survival in this interspecific population. The fine mapping of a previously reported rhizome QTL on sorghum chromosome SBI-01 was conducted by targeting this genomic region with additional simple sequence repeat markers. Fine mapping reduced the 2-LOD rhizome QTL interval from ~59 to ~14.5 Mb, which represents a 75 % reduction in physical distance and a 53 % reduction in the number of putative genes in the locus.

/pdf/targeted-mapping-of-quantitative-trait-locus-regions-for-1jfyfjwmxt.pdf

Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum population.

Synthetic apomixis with normal hybrid rice seed production.

Synthetic apomixis: the beginning of a new era.

Apomixis is an asexual mode of reproduction through seeds where progeny are clones of the mother plants. Naturally apomictic modes of reproduction are found in hundreds of plant genera distributed across more than 30 plant families, but are absent in major crop plants. Apomixis has the potential to be a breakthrough technology by allowing the propagation through seed of any genotype, including F1 hybrids. Here, we have summarized the recent progress toward synthetic apomixis, where combining targeted modifications of both the meiosis and fertilization processes leads to the production of clonal seeds at high frequencies. Despite some remaining challenges, the technology has approached a level of maturity that allows its consideration for application in the field. 

/pdf/engineering-apomixis-in-crops-1ofkbp53.pdf

Engineering apomixis in crops

Doubled haploid (DH) technology and synthetic apomixis approaches can greatly shorten breeding cycles and thereby enhance breeding efficiency. Compared with traditional breeding methods, DH technology offers the advantage of being able to rapidly generate inbred lines, while synthetic apomixis can effectively fix hybrid vigor. In this review, we focus on (i) recent advances in identifying and characterizing genes responsible for haploid induction (HI), (ii) the molecular mechanisms of HI, (iii) spontaneous genome doubling, and (iv) crop synthetic apomixis. We also discuss the challenges and potential solutions for future crop breeding programs utilizing DH technology and synthetic apomixis. Finally, we offer a perspective on integrating DH and synthetic apomixis within precision breeding and de novo domestication. 

Doubled Haploid Technology and Synthetic Apomixis: Recent Advances and Applications in Future Crop Breeding

A rhizomatous individual obtained from interspecific BC1F1 progenies between Oryza sativa and O. longistaminata.

Doubled haploid (DH) technology is an efficient strategy for producing completely homozygous lines for breeding programs. Mutations in the MATRILINEAL (MTL) phospholipase trigger intraspecific haploid induction in cereals. Although an in vivo haploid induction system based on OsMTL-edited plants has been established in rice (Oryza sativa), DH technology is still limited by other factors, such as haploid identification, which is one of the essential steps required for DH technology. In the study, we addressed this technical challenge by integrating specific molecular and phenotypic markers into rice haploid inducers. We first generated large fragment insertion or deletion mutations within the OsMTL gene and designed a pair of primers flanking the mutational sites to be used as the specific and universal molecular markers between wild-type and Osmtl plants. Next, we screened for hairy leaf as a single dominant trait and integrated it into specific molecular marker-based haploid inducers using the cross and self-cross method. When crossing cytoplasmic male sterile lines with these haploid inducers, we utilized the specific InDel marker and hairy leaf phenotypic marker to identify putative haploids (or double haploids). These putative haploids were further confirmed through ploidy and phenotypic analysis, demonstrating the high efficiency of haploid identification using these markers. The haploid induction rate (HIR) of the developed specific molecular and phenotypic marker-based haploid inducers ranged from 3.7% to 12.5%. We have achieved successful integration of distinct molecular and phenotypic markers into rice haploid inducers. Our advanced marker-based system has significantly enhanced the accuracy of haploid identification, thereby expediting the adoption of DH technology in rice breeding.

/pdf/development-of-specific-molecular-and-phenotypic-marker-2uh001g0.pdf

Development of Specific Molecular and Phenotypic Marker-Based Haploid Inducers in Rice

In hybrid plants, heterosis often produces large, vigorous plants with high yields; however, hybrid seeds are generated by costly and laborious crosses of inbred parents. Apomixis, in which a plant produces a clone of itself via asexual reproduction through seeds, may produce another revolution in plant biology. Recently, synthetic apomixis enabled clonal reproduction of F1 hybrids through seeds in rice (Oryza sativa), but the inheritance of the synthetic apomixis trait and superior heterotic phenotypes across generations remained unclear. Here, we propagated clonal plants to the T4 generation and investigated their genetic and molecular stability at each generation. By analyzing agronomic traits, as well as the genome, methylome, transcriptome, and allele-specific transcriptome, we showed that the descendant clonal plants remained stable. Unexpectedly, in addition to normal clonal seeds, the plants also produced a few aneuploids that had eliminated large genomic segments in each generation. Despite the identification of rare aneuploids, the observation that the synthetic apomixis trait is stably transmitted through multiple generations helps confirm the feasibility of using apomixis in the future. 

https://doi.org/10.1016/j.xplc.2022.100470

Synthetic apomixis enables stable transgenerational transmission of heterotic phenotypes in hybrid rice

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Synthetic apomixis: the beginning of a new era.

A rhizomatous individual obtained from interspecific BC1F1 progenies between Oryza sativa and O. longistaminata.

Development of Specific Molecular and Phenotypic Marker-Based Haploid Inducers in Rice

Synthetic apomixis enables stable transgenerational transmission of heterotic phenotypes in hybrid rice