Doubled haploid technology, which enables the generation of homozygous lines in a single step, is one of the modern tools being employed for accelerating breeding processes in different crops. In rice, a globally important staple food crop, doubled haploid production through androgenesis is increasingly being employed in breeding programs. Amongst the androgenic rice lines, doubled haploids are formed spontaneously at about 50–60%, while the remaining 40–50% of plants remain as haploids. As haploids cannot be easily identified, it is routine to grow all the rice androgenic lines till maturity and harvest the seeds from the fertile doubled haploids. Therefore, the methods that facilitate easy identification of haploids at an early developmental stage in rice would enable treatment of such haploid lines with colchicine, to increase the efficiency of doubled haploid production. Further, it would also help in eliminating the operational cost involved in maintaining them till maturity. In the above context, a systematic study to identify easily observable physiological and morphological differences between haploid and doubled haploid rice lines was undertaken. Rice haploids were found to be noticeably different from doubled haploids in photosynthetic rate, transpiration rate, stomatal conductance, and morphology of lodicules, stigma and style, features which have not been reported before. Most importantly, rice haploids invariably have acute leaf apex which is easily distinguishable from the doubled haploids that have attenuated leaf apex shape. Very high per cent accuracy in the prediction of ploidy level was observed when haploids were identified at an early developmental stage based on leaf apex shape, and the results verified with flow cytometry perfectly matches with leaf apex shape. The study establishes ‘acute leaf apex’ shape as an accurate visual marker to rapidly identify haploid rice lines at an early developmental stage in a cost-effective manner.

为了给今后西番莲等热带果树的单倍体育种研究提供理论指导,文章归纳了人工诱导孤雄生殖、人工诱导孤雌生殖、染色体加倍等不同单倍体育种培养技术的技术要点及发展现状,总结了单倍体育种技术在禾谷类作物、花卉、林木和果树育种方面的应用进展。同时指出,单倍体育种技术的发展有利于建立作物品种纯合系,推进遗传学研究,形成新的基因型,加快热带果树的育种进程。

Mixing maternal and paternal genomes in embryos is not only responsible for the evolutionary success of sexual reproduction, but is also a cornerstone of plant breeding. However, once an interesting gene combination is obtained, further genetic mixing is problematic. To rapidly fix genetic information, doubled haploid plants can be produced: haploid embryos having solely the genetic information from one parent are allowed to develop, and chromosome doubling generates fully homozygous plants. A powerful path to the production of doubled haploids is based on haploid inducer lines. A simple cross between a haploid inducer line and the line with gene combinations to be fixed will trigger haploid embryo development. However, the exact mechanism behind in planta haploid induction remains an enduring mystery. The recent discoveries of molecular actors triggering haploid induction in the maize crop and the model Arabidopsis thaliana pinpoint an essential role of processes related to gamete development, gamete interactions and genome stability. These findings enabled translation of haploid induction capacity to other crops as well as the use of haploid inducer lines to deliver genome editing machinery into various crop varieties. These recent advances not only hold promise for the next generations of plant breeding strategies, but they also provide a deeper insight into the fundamental bases of sexual reproduction in plants.

As one of the most important staple crops in the world, rice plays a pivotal role in world food security. The creation of doubled haploids based on anther culture is an important technology for rice breeding. However, at present, rice anther culture technology still faces many problems, such as genotype dependency, especially genotypes of indica rice. In this study, fifteen rice genotypes, including twelve japonica rice genotypes and three indica rice genotypes, were randomly selected and used to study anther culture by using a modified M8 medium. The results showed that the total callus induction rates of these different rice genotypes ranged from 0.81 to 13.95%, with an average of 6.64%, while the callus induction rates calculated for the top ten highest callus inductions for each rice genotype ranged from 2.75 to 17.00%, with an average of 10.56%. There were varying gaps between the total callus induction rates and the callus induction rates in these different rice genotypes. The fact that the gaps for some rice genotypes were relatively large indicated that standard tiller or anther collection was not applicable to all rice genotypes and that there was still a lot of room for improvement in the callus induction rate of some rice genotypes through optimization of the sampling method. The plantlet regeneration rates ranged from 12.55 to 456.54%, with an average of 200.10%. Although there were many albinos from anther culture for some rice genotypes, these would still meet the requirement if the rice genotypes had higher callus induction rates or regeneration rates. The percentages of seed setting of regenerated green seedlings ranged from 14% to 84%, with an average of 48.73%. Genetic diversity analysis showed that the genetic background of these different rice genotypes was representative, and the phylogenetic tree and Principal Component Analysis (PCA) divided them into indica and japonica types. Therefore, in this study, an anther culture method suitable for both indica and japonica rice genotypes was established, which could improve doubled haploid breeding in rice.

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.

花药培养技术的出现,大大地缩短了水稻育种的年限,也加快了各种基因型材料的获取。本研究综述了花药培养技术概况、影响花药培养力的6个关键因素、水稻花药培养技术的进展、分析水稻花药培养技术现阶段存在的问题,并对未来发展进行了展望。

Centromeres control chromosome inheritance in eukaryotes, yet their DNA structure and primary sequence are hypervariable. Most animals and plants have megabases of tandem repeats at their centromeres, unlike yeast with unique centromere sequences. Centromere function requires the centromere-specific histone CENH3 (CENP-A in human), which replaces histone H3 in centromeric nucleosomes. CENH3 evolves rapidly, particularly in its N-terminal tail domain. A portion of the CENH3 histone-fold domain, the CENP-A targeting domain (CATD), has been previously shown to confer kinetochore localization and centromere function when swapped into human H3. Furthermore, CENP-A in human cells can be functionally replaced by CENH3 from distantly related organisms including Saccharomyces cerevisiae. We have used cenh3-1 (a null mutant in Arabidopsis thaliana) to replace endogenous CENH3 with GFP-tagged variants. A H3.3 tail domain–CENH3 histone-fold domain chimera rescued viability of cenh3-1, but CENH3's lacking a tail domain were nonfunctional. In contrast to human results, H3 containing the A. thaliana CATD cannot complement cenh3-1. GFP–CENH3 from the sister species A. arenosa functionally replaces A. thaliana CENH3. GFP–CENH3 from the close relative Brassica rapa was targeted to centromeres, but did not complement cenh3-1, indicating that kinetochore localization and centromere function can be uncoupled. We conclude that CENH3 function in A. thaliana, an organism with large tandem repeat centromeres, has stringent requirements for functional complementation in mitosis.

R1-nj anthocyanin marker inhibition is highly frequent in tropical maize germplasm considerably affecting efficiency of haploid identification. Molecular markers reliably differentiating germplasm with anthocyanin color inhibitor have been identified in this study. The R1-Navajo (R1-nj) color marker facilitates easy and quick identification of haploid kernels at the seed stage during in vivo haploid induction process in maize. However, the Navajo phenotype can be completely suppressed or poorly expressed in some germplasm, making it impossible or inefficient to identify haploids at the seed stage. In this study, we characterized the expression of R1-nj marker in a large array of tropical/subtropical inbred lines, breeding populations and landraces by crossing with the R1-nj-based tropicalized haploid inducer. There was a high frequency of inhibition of the Navajo phenotype in the maize inbred lines, which are used in tropical breeding programs. Genome-wide association mapping showed that the C1 anthocyanin regulatory locus is the most significant genetic factor influencing inhibition of the Navajo phenotype. Molecular marker assays were designed based on polymorphism in the C1 vs C1-I alleles. Analysis of a set of 714 inbred lines demonstrated that a combination of two gene-specific markers--8 bp C1-I InDel and C1-I SNP--could predict with high accuracy the presence of anthocyanin color inhibition in the germplasm analyzed. Information generated in this study aids in making informed decisions on the constitution of source populations for doubled haploid (DH) line development in tropical germplasm, particularly those derived from elite maize lines from CIMMYT. The C1-I gene-specific molecular markers identified and validated will facilitate high-throughput and cost-effective evaluation of a large pool of germplasm for the presence of the dominant color inhibitor in maize germplasm.

\n One of the critical limitations for the in vivo production of doubled haploid (DH) lines in maize (\n Zea mays\n L.) is the inability to effectively identify haploids in a significant proportion of induction crosses due to the possibility of complete or partial inhibition of the currently used\n R1‐nj\n (Navajo) color marker. In this study, we demonstrate that the\n R1‐nj\n marker could result in a high proportion of false positives among the haploids identified, besides being ineffective in germplasm with natural anthocyanin expression in pericarp tissue. To address these limitations, we developed haploid inducer lines with triple anthocyanin color markers, including the expression of anthocyanin coloration in the seedling roots and leaf sheaths, in addition to the Navajo marker on the seed. Although these inducers show acceptable haploid induction rates ranging from 8.6 to 10.2%, they exhibited relatively poor agronomic performance compared with tropicalized haploid inducers within tropical environments. The addition of the red root marker more accurately identified haploids among the germinating seedlings, including four tropical inbred lines and eight breeding populations that showed complete inhibition of\n R1‐nj\n. We also demonstrate that the red root marker can be used for haploid identification in germplasm with natural anthocyanin expression in the pericarp. A survey of 546 tropical inbreds and 244 landraces showed that anthocyanin accumulation in the roots of germinating seedlings is very rare compared with anthocyanin accumulation in the seed and leaf sheath tissues. As a result, the red root marker can serve as a highly complementary marker to\n R1‐nj\n to enable effective identification of haploids within a wide range of tropical maize germplasm.\n

Manipulating grain size demonstrates great potential for yield promotion in cereals since it is tightly associated with grain weight. Several pathways modulating grain size have been elaborated in rice, but possible crosstalk between the ingredients is rarely studied. OsmiR396 negatively regulates grain size through targeting OsGRF4 (GS2) and OsGRF8, and proves to be multi-functioning. Here we showed that expression of GS3 gene, a Gγ-protein encoding gene, that negatively regulates grain size, was greatly down-regulated in the young embryos of MIM396, GRF8OE and GS2OE plants, indicating possible regulation of GS3 gene by OsmiR396/GRF module. Meanwhile, multiple biochemical assays proved possible transcriptional regulation of OsGRF4 and OsGRF8 proteins on GS3 gene. Further genetic relation analysis revealed tight genetic association between not only OsmiR396 and GS3 gene, but also GS2 and GS3 gene. Moreover, we revealed possible regulation of GS2 on four other grain size-regulating G protein encoding genes. Thus, the OsmiR396 pathway and the G protein pathway cross talks to regulate grain size. Therefore, we established a bridge linking the miRNA-transcription factors pathway and the G-protein signaling pathway that regulates grain size in rice.© 2024. The Author(s).

In vivo doubled haploid (DH) production based on crossing heterozygous germplasm with mtl haploid inducer lines promises to transform modern rice (Oryza sativa) breeding. However, this technology is limited, as haploid inducers and pollen acceptors have asynchronous heading dates. To address this obstacle, we developed a panel of multiple-heading-date mtl haploid inducer lines that produce pollen for more than 35 days. We edited the MTL gene in a hybrid rice with the CRISPR-Cas9 system. We then selected transgene-free homozygous mutants in the T1 generation and reproduced to T4 generation by single-seed descent method. We obtained 547 mtl haploid inducers with diverse heading dates (from 73 to 110 days) and selected 16 lines comprising a core population with continuous flowering. The seed-setting rate and haploid induction rate (HIR) of the core panel were 4.0–12.7% and 2.8–12.0%, respectively. Thus, our strategy of using multiple-heading-date mtl haploid inducers could accelerate the use of in vivo DH technology in rice breeding.

\n Doubled haploid technology has been widely applied to multiple plant species and is recognized as one of the most important technologies for improving crop breeding efficiency. Although mutations in\n MATRILINEAL/Zea mays PHOSPHOLIPASE A1/NOT LIKE DAD\n (\n MTL/ZmPLA1/NLD\n ) and\n Zea mays DOMAIN OF UNKNOWN FUNCTION 679 MEMBRANE PROTEIN\n (\n ZmDMP\n ) have been shown to generate haploids in maize, knowledge of the genetic basis of haploid induction (HI) remains incomplete. Therefore, cloning of new genes underlying HI is important for further elucidating its genetic architecture. Here, we found that loss-of-function mutations of\n Zea mays PHOSPHOLIPASE D3\n (\n ZmPLD3\n ), one of the members from the phospholipase D subfamily, could trigger maternal HI in maize.\n ZmPLD3\n was identified through a reverse genetic strategy based on analysis of pollen-specifically expressed phospholipases, followed by validation through the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR–Cas9) system. Mutations of\n ZmPLD3\n resulted in a haploid induction rate (HIR) similar to that of\n mtl/zmpla1/nld\n and showed synergistic effects rather than functional redundancy on tripling the HIR (from 1.19% to 4.13%) in the presence of\n mtl/zmpla1/nld\n. RNA-seq profiling of mature pollen indicated that a large number of pollen-specific differentially expressed genes were enriched in processes related to gametogenesis development, such as pollen tube development and cell communication, during the double-fertilization process. In addition,\n ZmPLD3\n is highly conserved among cereals, highlighting the potential application of these in vivo haploid-inducer lines for other important crop plant species. Collectively, our discovery identifies a novel gene underlying in vivo maternal HI and provides possibility of breeding haploid inducers with further improved HIR.\n

【目的】探究水稻DMP家族基因的单倍体诱导能力，为单倍体育种提供新的基因资源。【方法】筛选与ZmDMP基因高同源且在花粉中高表达的水稻DMP家族基因作为候选基因；利用CRISPR/Cas9多基因编辑技术，在籼粳杂交稻“春优84”中对筛选的DMP家族基因和单倍体诱导基因OsMTL创制单基因敲除以及多基因组合敲除突变体；对突变体进行形态学观察和花粉育性鉴定；调查统计转基因T₀材料的结实率和单倍体诱导率。【结果】在水稻RAP-DB数据库中共检索到13个玉米单倍体诱导基因ZmDMP的同源基因。OsDMP1和OsDMP2与ZmDMP同源性最高，相似度分别为41.24% 和37.32%；OsDMP1和OsDMP3在花药中表达量最高。因此，选择OsDMP1、OsDMP2、OsDMP3基因为候选基因。通过CRISPR/Cas9基因编辑技术创制了OsDMP1、OsDMP2、OsDMP3的单基因敲除和组合敲除突变体(osdmp1、osdmp2、osdmp3、osdmp1-osdmp2、osdmp1-osdmp3、osdmp1-osdmp2-osdmp3)，OsMTL单基因敲除突变体(osmtl)，以及OsDMP1、OsDMP2、OsDMP3与OsMTL基因的组合敲除突变体(osmtl-osdmp1、osmtl-osdmp2、osmtl-osdmp3、osmtl-osdmp1-osdmp2、osmtl-osdmp1-osdmp3、osmtl- osdmp1-osdmp2-osdmp3)。表型考察发现，相比较野生型，所有突变体的植株形态和花粉育性均未发生显著变化，而仅在包含osmtl的单基因敲除和多基因组合敲除突变体中结实率发生显著下降。单倍体鉴定结果显示，OsDMP1、OsDMP2、OsDMP3与OsMTL组合突变的单倍体诱导效率分别为0.4% ± 0.6%、2.6% ± 2.8%、1.4% ± 0.6%、1.5% ±1.3%、2.1% ± 2.4%、2.2% ± 0.6%，与osmtl突变体(1.5% ± 0.5%)无显著差异。然而，当OsDMP家族基因单个突变或多个组合突变时均无单倍体产生。【结论】本研究利用CRISPR/Cas9基因编辑技术成功创制了水稻OsDMP1、OsDMP2、OsDMP3、OsMTL单基因和多基因组合敲除突变体，发现了OsDMP1、OsDMP2和OsDMP3均无独立单倍体诱导能力，也不能提升OsMTL基因的单倍体诱导效率。本研究促进了对水稻中OsDMP同源基因的了解，为后续单倍体诱导基因研究提供参考。

Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.© 2024 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

综述了诱导单倍体产生的花药培养、远缘杂交、诱导系、着丝粒介导等途径,及其在加速育种进程、构建DH群体、非同源染色体配对研究、转基因供体、突变体研究及基因组测序中的作用。

通过常规杂交育种结合分子标记辅助选择和花药培养技术,快速获得携带抗白叶枯病Xa39基因的水稻籼型恢复系。通过选系测配筛选出1个高抗白叶枯病的恢复系,命名为嘉浙恢08,采用白叶枯菌种对嘉浙恢08及其杂交组合进行田间接种。结果表明,嘉浙恢08及所配制的杂交组合抗病性强,并且杂交组合具有良好的产量潜力。

杂交水稻研究与应用是中国科学家对全世界粮食安全保障做出的一项重要历史贡献。我国对杂交粳稻的研究虽迟于日本,但却后来居上,并领先于其他国家。更重要的是,中国杂交粳稻研究还推动了籼粳亚种间杂交亲和性的研究,选育了大量以“甬优”系列为代表的、利用亚种间优势的超高产籼粳杂交稻组合,为中国粮食安全提供了足够的种子“芯片”。本文回顾了中国杂交粳稻研究历程,重点分析了杂交粳稻研究中的每个创新思维,希望引起对杂交粳稻研究的讨论,“抛砖引玉”,寻找杂交粳稻实际育种规律,使大田真正育种效率得到更大地提高。

Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild-type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars.© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.