Genetic analysis and fine mapping of tms9, a novel thermosensitive genic male‐sterile gene in rice (Oryza sativa L.)

Two‐line hybrid rice as a novel hybrid breeding method has huge potential for yield increasing and utilization of intersubspecific heterosis, and it is of major significance for the food security of rice‐consuming populations. Zhu1S is a thermosensitive genic male‐sterile line of rice with low critical temperature and excellent combining ability, which has been widely exploited as a female parent in Chinese two‐line hybrid rice breeding. Here, genetic mapping in F₂ populations was used to show that its male sterility is inherited as a single recessive gene and that responsible gene (termed tms9) lies on the short arm of chromosome 2. A high‐resolution linkage analysis which was based on the Zhu1S/R173 F₂ population found that the thermosensitive genic male‐sterile gene tms9 of Zhu1S was fine mapped between insertion–deletion (Indel) markers Indel 37 and Indel 57, and the genetic distance from the tms9 to the two markers was 0.12 and 0.31 cM, respectively. The physical distance between the two markers was about 107.2 kb. Sequence annotation databases showed that the two Indel markers (Indel 37 and Indel 57) were located on two BAC clones (B1307A11 and P0027A02). There are sixteen open reading frames (ORF) present in this region. The results of this study are of great significance for further cloning tms9 and molecular marker–assisted selection.     

Development of broad‐spectrum bacterial blight resistance into thermo‐sensitive genic male sterile lines

Two‐line hybrid rice technology is an effective way to increase rice production and improve rice quality. In this study, three bacterial blight (BB) resistance genes, Xa7, Xa21 and Xa23, were introgressed separately into C815S, a popular thermo‐sensitive genic male sterile (TGMS) line to develop five BB‐resistant lines (Hua1005S, Hua1002S, Hua1009S, Hua1006S and Hua1001S) to be resistant against seven races of Xanthomonas oryzae pv. oryzae (Xoo). The two‐line hybrids with heterozygous Xa23 were resistant against seven Xoo strains. But, the hybrids with heterozygous loci for both Xa7 and Xa21 were only resistant against three Xoo strains and were moderately susceptible to the other four strains indicating the role of modifiers influencing the poor expression of dominant BB resistance genes under heterozygous state. Among them, Hua1006S was found to be a promising TGMS line with its higher degree of disease resistance level on account of broad‐spectrum resistance gene Xa23 besides possessing better plant type and rice grain quality features.     

Mapping of male sterility gene ms10 in chilli pepper (Capsicum annuum L.)

Most of the hybrid seed in chilli are produced manually, but the use of male sterility (MS) can reduce the cost of hybrid seed production. MS‐12, a nuclear male‐sterile (NMS) line developed at Punjab Agricultural University, Ludhiana (India), has been utilized to develop commercial F₁ hybrids. A recessive gene, designated as ms10, governs MS in MS‐12. Due to recessive gene control, development of new NMS lines incorporating ms10 gene is tedious and time‐consuming. We identified SSR markers AVRDC‐PP12 and AVRDC_MD997* linked to the ms10 gene. A total of 558 primer pairs were screened following bulked segregant analysis (BSA). Linkage analysis in 210 F₂ plants indicated that the two SSR markers were linked to the ms10 gene and the marker AVRDC‐PP12 was closest to the gene at 7.2 cM distance. The marker was mapped to chromosome 1 at genome position 175 694 513 to 175 694 644. Until more closely linked markers are developed, the marker AVRDC‐PP12 would facilitate transfer of ms10 gene through marker‐assisted selection (MAS). Fine mapping would lead to cloning of the ms10 gene.     

Comparative Study of CaMsrB2 Gene Containing Drought‐Tolerant Transgenic Rice (Oryza sativa L.) and Non‐Transgenic Counterpart

Concerns regarding the safety of transgenic foods have been raised because of possibility of undesirable effects development during genetic engineering. Analysis of phenotypic traits can increase the likelihoods of identifying those unintended effects in dietary composition of the GM crops. Objective of this study was to compare the transgenic lines with their non‐transgenic counterpart. Different vegetative and reproductive traits as well as antioxidant properties were considered to evaluate the transgenic (HV8 and HV23) lines containing CaMsrB2 gene and their non‐transgenic (Ilmi) parent line. Grain size and weight, seed germination, root length, root and shoot dry weight, length and width of flag leaf, plant height, and ligule, stamen and carpel length were not significantly different. Onset and completion of heading in each line occurred almost during the same period. The antioxidant properties in terms of DPPH (1,1‐diphenyl‐2‐picrylhydrazyl) radical scavenging activity and polyphenol content were not statistically different under same treatment condition. The results suggested that the transgenic rice lines containing CaMsrB2 gene were equivalent to their non‐transgenic counterpart without any visible unintended effects.     

Development of dominant nuclear male-sterile lines with a blue seed marker in durum and common wheat

In order to develop genie male‐sterile lines with a blue seed marker, male‐sterile plants, controlled by a dominant nuclear gene Ms2, were used as female parents against a 4E disomic addition line ‘Xiaoyan Lanli’(2n= 44, AABBDD+4EII) as the male parent to produce monosomic addition lines with blue seed. Male‐sterile plants from the monosomic addition lines were pollinated with durum wheat for several generations and in 1989 a male‐sterile line with the blue grain gene and the male‐sterile gene Ms2 on the same additional chromosome was detected and named line 89‐2343. Using this line, the blue seed marker was successfully added to a short male‐sterile line containing Ms2 and Rht10. The segregation ratios of male sterility and seed colour as well as the chromosome figurations of different plants indicated that the blue grain genes, Ms2 and Rht10 were located on the same additional chromosome. Cytological analysis showed that the blue marker male‐sterile lines in durum wheat and common wheat were monosomic with an additional chromosome 4E. The inheritance ratio for blue seed male‐sterile plants and white seed male‐fertile plants was 19.7% and 80.3%, respectively, in common wheat. The potential for using blue marker sterile lines in population improvement and hybrid production is discussed.     

Breeding of transgenic rice restorer line for multiple resistance against bacterial blight, striped stem borer and herbicide

In this paper, we described the breeding of transgenic rice restorer line for multiple resistance against bacterial blight, striped stem borer (SSB) and herbicide by conventional crossing of two transgenic parental lines transformed independently with different genes. Two stable transgenic rice lines used as donor parents were developed, one was Zhongguo91 which contained cry1Ab gene (for insect resistance) and bar gene (for tolerance of herbicide), and the other was Yujing6 which contained Xa21 gene (resistance to bacterial blight). The elite restorer line Hui773 was used as recipient and crossed with the two stable transgenic rice lines. Then five successive backcrosses were made using Hui773 as recurrent parent. Two rice elite restorers, T773-1 expressing cry1Ab and bar genes and T773-2 expressing Xa21 gene, were obtained, which were confirmed by PCR analysis and testing selectable marker genes in the hybrid progenies. The cross was made between T773-1 and T773-2 to select stable restorer line carrying Xa21, cry1Ab and bar genes. Finally, we obtained transgenic restorer line T773 with good agronomic traits and obvious multiple resistance to Xanthomonas oryzae pv. oryzae, striped stem borer (Chilo suppressalis) and herbicide. The hybrid F₁ generation produced from the cross between transgenic restorer line T773 and a corresponding male sterile line Zaohua2A maintained obvious resistance to rice bacterial blight, rice leaffolder and striped stem borer, and showed significant heterosis. Our results indicate that it is feasible to develop transgenic hybrid rice cultivar through breeding transgenic restorer lines.     

Development of chloroplast‐specific microsatellite markers for molecular characterization of alloplasmic lines and phylogenetic analysis in wheat

Wheat (Triticum aestivum L.) is strictly a self‐pollinated crop, where hybrid breeding requires well‐characterized cytoplasmic male sterile (CMS) lines. The CMS has mostly been developed by substituting nuclear genome of wheat into the cytoplasm from wild relatives. Molecular characterization of 90 genotypes including 82 CMS lines originating from five different species, namely Aegilops speltoides, Ae. kotschyi, Ae. variabilis, Triticum araraticum and T. timopheevii, and eight popular varieties was carried out. Consequently, a set of 25 microsatellite markers specific to chloroplast (cpSSRs) were designed and successfully validated for specificity of amplification. A total of 15 cpSSRs (60%) were found polymorphic, of which three cpSSRs (TaCM7, TaCM8 and TaCM11) in genic region and twelve cpSSRs were located in intergenic region. Phylogenetic analysis of genotypes using cpSSRs revealed two major groups well in accordance with respective origin. A set of cpSSRs and phylogeny of CMS belonging to different origins developed, which will be helpful for the improvement in CMS system in wheat. The genic cpSSRs can be used for the allele mining and evolutionary studies.     

QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

Hybrid rice has contributed substantially to the improvement of grain production worldwide, yet its poor cooking and tasting characteristics have long been recognized. In this study, 132 recombinant inbred lines derived from LYPJ were used to identify quantitative trait loci (QTLs) for 12 cooking traits with the high‐density SNP linkage map recently developed by our team. We identified 17 QTLs on chromosomes 1, 2, 4, 5, 6, 7, 8, 9 and 11, which accounted for 7.50% to 23.50% of the phenotypic variations. A novel major QTL qBGL7 for boiled grain length was further fine‐mapped to an interval of 440 Kb between the two markers RM21906 and gl3 using a BC₃F₂ population. Two near‐isogenic lines with extreme boiled grain length, GX5‐176 and GX5‐101, could be directly used in improving cooking quality. We also identified a QTL for soaked grain width expansion rate, qSGWE6, in the Wx gene region on chromosome 6. The Wx differential regulation coincided with sequential variation between the two parents. Our work offered a theoretical basis for molecular breeding of high‐quality hybrid rice.     

The transformation of the photo-thermo sensitive genic male-sterile line 261S of rice via an expression vector containing the anti-Waxy gene

Transgenic photo-thermo sensitive genic male sterility Oryza sativa L. cv. “261S” plants with the anti-Waxy gene were successfully obtained using an Agrobacterium tumefaciens-mediated co-transformation method. Marker-free homozygous transgenic lines with the anti-Waxy gene were obtained. The setting seed rates of the transgenic plants via self-pollination or via crossing with the restorer line WX99075 rice and the 1000-grain weight of the transgenic plants and the F₂ hybrid seeds obtained by crossing the transgenic or non-transgenic plants with the restorer line WX99075 rice, and the number of panicles of the transgenic plants and yields of the F₂ hybrid rice, were analysed. Quality indexes of the transgenic plants and of the F₂ hybrid seeds were analysed. Our researches results indicate that hybrid female and hybrid descendant edibility could be improved via the introduction of the anti-Waxy gene, but the grain yields of the reserve seeds via self-pollination of the transgenic photo-thermo sensitive genic sterile lines and of the hybrid rice were not affected.     

Maternal inheritance of male sterility in the progeny of a natural hybrid between Cajanus lineatus and C. cajan

Adoption of pigeonpea hybrids in central and southern India is showing high impact with on‐farm yield advantages of >30%. The hybrid pigeonpea technology, the first in any legume crop, is based on a cytoplasmic‐nuclear male‐sterility (CMS) system. For a long‐term sustainability of hybrid programme, it is imperative that both nuclear diversity and cytoplasmic diversity are maintained among hybrid parents. In this context, a continuous search for new CMS‐inducing cytoplasms is necessary. This paper reports detection of maternal inheritance of male sterility in the progeny derived from a natural hybrid between a wild relative [Cajanus lineatus (W. & A.) Maesen comb. nov.] of pigeonpea and an unknown pigeonpea [Cajanus cajan (L.) Millsp.] genotype. In the present study, the male sterility was maintained up to BC₇F₁ generation by an advanced breeding pigeonpea line ICPL 99044. This male sterility inducing cytoplasm of C. lineatus was tagged as A₆. In future, this CMS genetic stock can be used to develop a range of new pigeonpea hybrids with high yield and adaptation.     

Variations in chlorosis and potential usefulness of alloplasmic Brassica rapa with the cytoplasm of male sterile Brassica juncea

To select superior seed parents for vegetable hybrid seed production, we conducted interspecific crosses between male sterile Brassica juncea (2n = 36, AABB) and eight inbred lines of Brassica rapa (2n = 20, AA). Alloplasmic lines of B. rapa with the cytoplasm of B. juncea were developed from B. juncea × B. rapa hybrids by repeated backcrossing using B. rapa as the recurrent male parent until the BC₃ generation. Seed fertility, male sterility and chlorophyll content were investigated in these plants cultivated under four different temperature conditions (5, 10, 12 and 20°C). At 10°C, the alloplasmic lines of B. rapa with the cytoplasm of B. juncea were male sterile with partly chlorotic leaves. The alloplasmic B. rapa had lower chlorophyll a, chlorophyll b and carotenoid contents than those of the original B. rapa. The leaves recovered from chlorosis when the plants were cultivated at 20°C. An alloplasmic line of B. rapa (A6) is available as a seed parent for vegetable hybrid seed production and contributes seed fertility, slight chlorosis and stable male sterility.     

Marker‐assisted selection for rice blast resistance genes Pi2 and Pi9 through high‐resolution melting of a gene‐targeted amplicon

The use of host resistance (R) genes is considered the most cost‐effective option to control the rice blast disease. The two allelic R genes Pi2 and Pi9 confer very broad‐spectrum resistance against blast isolates collected worldwide. However, the two genes have not yet been widely deployed in rice breeding programmes. Availability of specific markers for them would facilitate incorporating the two R genes into new rice lines through marker‐assisted selection. Herein, we report the development and utilization of a robust and specific marker for the Pi2 and Pi9. This marker was derived from polymorphisms within the target gene, and achieved simultaneously distinguish Pi2 and Pi9 from other alleles through high‐resolution melting of a small amplicon. With the marker, we were able to transfer the Pi2 into an elite restorer line through marker‐assisted backcrossing, successfully obtained effective resistance to blast disease, and we were also able to, respectively, incorporate the Pi2 and Pi9 with two other R genes. As the additive effect, blast resistance in these stacking lines harbouring three R genes were significantly improved.     

Effect of alien cytoplasm and fertility restorer genes on agronomic and physiological traits of Brassica juncea (L.) Czern

To assess the effect of alien cytoplasm and fertility restorer genes on agronomic and physiological traits in Brassica juncea, cytoplasmic male sterile (CMS) and fertility restorer lines involving five alloplasms in three nuclear backgrounds were constituted through repeated backcrossing. These lines were evaluated along with euplasmic lines for agronomic traits in field experiments. Respiration efficiency of in vitro cultured hypocotyls, and chlorophyll content in leaves were also estimated. Significant adverse effects of trachystoma and catholica cytoplasms on yield‐contributing traits and yield were noticed. The restorer gene corrected the floral defects in CMS trachystoma and restored yield to the level of euplasmic line, while it did so only partly in CMS catholica. Restorer genes had no adverse effect on traits in any of the systems. On the contrary, the Rf gene of moricandia CMS system exerted a positive effect on leaf chlorophyll content. Likewise, in vitro assay indicated the moricandia CMS system as vigorous. The moricandia CMS plants gave higher seed yield perhaps due to overall better vigour and higher leaf chlorophyll content.     

Production of a desirable Brassica oleracea CMS line using an alloplasmic B. rapa CMS line carrying Diplotaxis erucoides cytoplasm as a bridge plant

In Brassica oleracea, production of F₁ hybrid seeds mainly makes use of the improved Ogura cytoplasmic male sterile (CMS) line. However, reliance on one particular line is a risk, and it would be advantageous to develop other CMS lines. In this study, we transferred Diplotaxis erucoides cytoplasm to B. oleracea cultivars using an alloplasmic B. rapaCMS line as a bridge plant to avoid incompatibility between donor and recipient plants. The new B. oleraceaCMS lines, which were derived by four generations of backcrossing, had small rudimentary anthers with no pollen grain and showed complete male sterility. There was no functional defect in other floral organs, and the ability to receive normal pollen did not appear to be impaired. Moreover, the B. oleraceaCMS lines carrying D. erucoides cytoplasm had larger leaf areas and a normal plastochron. As a consequence, the B. oleraceaCMS lines carrying D. erucoides cytoplasm have the potential to be valuable alternatives for use in commercial B. oleracea hybrid seed production.     

Role of male-sterile cytoplasm in resistance to barley yellow mosaic virus and Fusarium head blight in barley

Two types of male‐sterile cytoplasm, designated msm1 and msm2, in barley were investigated to determine whether these cytoplasms confer resistance to barley yellow mosaic virus (Ba YMV) and Fusarium head blight (FHB). Alloplasmic lines and isogenic lines of two cultivars showed the same reaction to each Ba YMV as that of their euplasmic lines. This demonstrates that the barley male‐sterile cytoplasms msm1 and msm2 have no effect on resistance to BaYMV. No significant difference in reactions to FHB was recognized among fertile alloplasmic lines of ‘Adorra’, but the difference in reactions to FHB between fertile and sterile isogenic lines of ‘Adorra’ was significant. The damage caused by FHB in the male‐sterile lines that produced sterile pollen was significantly greater than the damage in a sterile line that did not produce pollen. These results suggest that pollen or anthers are important factors in infection with or spread of FHB. For production of hybrid seeds, male‐sterile lines with no pollen production, such as those with msm1 male‐sterile cytoplasm, would reduce FHB infestation.     

Improving male fertility restoration of common wheat for Triticum timopheevii cytoplasm

The fertile pure line R3‐37 of common wheat with cytoplasm of Triticum timopheevii Zhuk. is an R‐line (restorer) that can restore the male fertility of A‐lines (male sterile lines) with T. timopheevii cytoplasm. In breeding hybrid wheat, the hybrid of the cross R3‐37/ Baimian3 was found to be completely male sterile, indicating that Baimian3 has some genes that are epistatic to the Rf genes in R3‐37. In order to elucidate the essence of this phenomenon, the male fertilities of the hybrids of 27 crosses including R3‐37 and/or Baimian3 were studied. The results show that inheritance of male fertility of the hybrid R3‐37/Baimian3 involves interactions among Rf alleles, male fertility‐inhibiting genes and genetic background. Although more than 70 different kinds of male sterile cytoplasm to common wheat have been discovered, the systems of hybrid wheat production based on male sterile cytoplasm are all the A‐line/R‐line type and all have similar problems of hybrid fertility restoration. This study confirmed that there is a new model (A‐line/R*‐line//R‐line) for producing hybrid wheat with high fertility restoration. In the new model, the completely male sterile hybrids of A‐line/R*‐line can act as common A‐line.     

Developing rice lines possessing neutral alleles at sterility loci to improve the width of compatibility

To improve the width of compatibility for overcoming various sterilities in inter‐subspecific hybrid rice, some elite lines combining several sterility‐neutral genes were developed and the effects on mitigating various hybrid sterilities were tested. From Akihikari// IR36/Dular, neutral genes at ga11 and six sterility loci, S5, S7, S8, S9, S15 and S16, were combined and elite lines were obtained in their successive progeny. Four of the lines tested were confirmed to combine the neutral alleles S5‐n, S7‐n, S8‐n, S9‐n, S15‐n and S16‐n at the sterility loci and, among them, two harboured an additional gamete abortion‐neutral allele, ga11‐n. F₁s, which used the lines and various testers as parents, mitigated the spikelet sterilities by six sterility loci and gamete abortion by a gametophyte gene, ga11. These lines could be selectively used as parents or donors to increase the width of compatibility of rice varieties for improving fertility in inter‐subspecific hybrid rice breeding.     

利用CRISPR/Cas9技术编辑水稻温敏不育基因TMS5

Thermo-sensitive genic male-sterile (TGMS) gene tms5 is most widely used in the two-line hybrid breeding system in China. To develop novel rice thermo-sensitive male sterile lines, we knocked out the TMS5 genes of six elite japonica and four indica rice varieties by using CRISPR/Cas9 gene editing technology. By analyzing the critical sterility-inducing temperature (CIST) of the newly TGMS lines, it was found that the CIST of japonica TGMS lines ZG75S, CYGS, YG0618S, ZG07S, T0361S, and 7679S were between 28°C and 32°C, the CIST of indica TGMS lines 2537S, 6150S and 6379S were between 24°C and 28°C, and the CIST of indica TGMS line 1109S was lower than 23.5°C. These results indicated that the CIST of tms5 mutant from different genetic background materials was different. The TGMS lines with lower CIST could be obtained by knocking out the TMS5 from different genetic background materials. A hybrid rice combination 1109S/8048 had high quality and high yield. The yield of 1109S/8048 was 13.1% higher than that of Fengliangyou 4. The creation of the TGMS 1109S and the high-yield cross combination 1109S/8048 provides a new way for high-yield breeding.     

Marker‐assisted introgression of bacterial blight and blast resistance into IR 58025B,an elite maintainer line of rice

IR 58025A is a very popular wild‐abortive cytoplasmic male sterile (WA‐CMS) line of rice and is extensively used for hybrid rice breeding. However, IR 58025A and many hybrids derived from it possess mild aroma (undesirable in some parts of India) and are highly susceptible to bacterial blight (BB) and blast diseases. To improve IR 58025A for BB and blast resistance, we have introgressed a major dominant gene conferring resistance against BB (i.e. Xa21) and blast (i.e. Pi54) into IR 58025B, the maintainer line of IR 58025A. An introgression line of Samba Mahsuri (i.e. SM2154) possessing Xa21 and Pi54 genes in homozygous condition and fine‐grain type was used as donor parent, and backcross breeding strategy was adopted for targeted introgression of the resistance genes. PCR‐based molecular markers tightly linked to Xa21 and Pi54 were used for selection of BB‐ and blast‐resistant lines, while closely linked markers were used for identification of backcross‐derived plants devoid of Rf4 and aroma. At BC₂F₅, four backcross‐derived lines possessing resistance against BB and blast, devoid of aroma, high yield, short plant stature, long‐slender grain type and with recurrent parent genome recovery ranging from 88.8% to 98.6% were selected and advanced for further evaluation. The improved versions of IR 58025B, viz. SB54‐11‐143‐9‐44‐5, SB54‐11‐143‐9‐44‐98, SB54‐11‐143‐9‐44‐111 and SB54‐11‐143‐9‐44‐171, behaved as perfect maintainers when test‐crossed with WA‐CMS lines. Agronomically superior lines of improved IR 58025B are being converted to CMS line through backcrossing for developing high‐yielding and biotic stress‐resistant rice hybrids.