Synergizing breeding strategies via combining speed breeding, phenotypic selection, and marker-assisted backcrossing for the introgression of Glu-B1i in wheat.

Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 near-isogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking.

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing.

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers' preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

Utilization of marker-assisted backcrossing to generate new gynoecious cucumber lines with genetic heritage similar to the indigenous Vietnamese cucumber.

The marker-assisted backcrossing (MAB) can help to transfer an interested allele at a target locus from a donor to a recipient line. Gynoecious is a pivotal trait of cucumber since commercial F1 hybrid seeds produced with gynoecious line as one of the parents are high-yield and affordable. This study aims to transfer the F locus encoded for gynoecious trait to Vietnamese domesticated cucumbers by marker-assisted backcrossing. Two monoecious cucumber lines, A1 (Ha Giang, Vietnam) A2 (Yen Bai, Vietnam), and two gynoecious cucumber lines, B1 (Plantgene, India) and B2 (Hue, Vietnam) were utilized as the starting materials. BCAT marker (located on the F locus) and 52 SSRs (spread across seven chromosomes and tightly linked with some crucial horticultural traits) were used as the foreground and background markers, respectively. With this, phenotype selection for fruit and leaf sizes was also applied. First, using phenotypic screening and foreground marker, A1 (Ha Giang, Vietnam) and B1 (Plantgene, India) were selected as donor and recurrent parents for backcrossing. Then, after two backcrosses followed by two self-pollinations, four gynoecious C cucumber lines were created. These C lines have leaf sizes slightly bigger than the recurrent parent. Importantly, their fruit length is the same or longer than A1 (Ha Giang, Vietnam). These new gynoecious lines could be used as material lines for producing commercial F1 hybrid seeds. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01481-w.

Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach

Abstract Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.

Resumo A mancha bacteriana das folhas (BLB) é uma das principais doenças do arroz na Malásia. Essa doença causa perdas substanciais de rendimento de até 70%. O desenvolvimento de variedades de arroz que herdaram características de resistência ao BLB é uma abordagem crucial para promover e sustentar a indústria do arroz na Malásia. Portanto, o objetivo deste estudo foi aumentar os caracteres BLB resistentes a doenças da variedade comercial MR219 de alto rendimento por meio de uma abordagem de cruzamento retrocruzamento com ferramenta de apoio de seleção assistida por marcador (MAS). O gene de resistência a BLB de amplo espectro, Xa7 do pai doador IRBB7, foi introgressado no MR219 suscetível (pai recorrente) usando dois marcadores flanqueadores ID7 e ID15. No BC3F4, conseguimos gerar 19 linhagens introgressadas com o gene Xa7 homozigoto e apresentamos características de resistência como genitor doador quando desafiado com Xanthomonas oryzae pv. oryzae por inoculação artificial. O pai recorrente MR219 e a variedade controle, MR263, estavam gravemente infectados pela doença. As linhas melhoradas exibiram características morfológicas e de desempenho de rendimento semelhantes às da variedade elite, MR219. Duas linhas, PB-2-107 e PB-2-34, foram escolhidas como linhas potenciais por causa de seus desempenhos excelentes em comparação com a mãe, MR219. Este estudo demonstra uma história de sucesso de aplicação de MAS no desenvolvimento de linhas de arroz melhoradas com resistência a doenças contra a doença BLB.

Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach / Introdução do gene resistente à ferragem da folha bacteriana (BLB), xa7 na variedade MARDI elite, MR219 por abordagem de backcrossing assistida por marcador (MABC)

Abstract Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.

Resumo A mancha bacteriana das folhas (BLB) é uma das principais doenças do arroz na Malásia. Essa doença causa perdas substanciais de rendimento de até 70%. O desenvolvimento de variedades de arroz que herdaram características de resistência ao BLB é uma abordagem crucial para promover e sustentar a indústria do arroz na Malásia. Portanto, o objetivo deste estudo foi aumentar os caracteres BLB resistentes a doenças da variedade comercial MR219 de alto rendimento por meio de uma abordagem de cruzamento retrocruzamento com ferramenta de apoio de seleção assistida por marcador (MAS). O gene de resistência a BLB de amplo espectro, Xa7 do pai doador IRBB7, foi introgressado no MR219 suscetível (pai recorrente) usando dois marcadores flanqueadores ID7 e ID15. No BC3F4, conseguimos gerar 19 linhagens introgressadas com o gene Xa7 homozigoto e apresentamos características de resistência como genitor doador quando desafiado com Xanthomonas oryzae pv. oryzae por inoculação artificial. O pai recorrente MR219 e a variedade controle, MR263, estavam gravemente infectados pela doença. As linhas melhoradas exibiram características morfológicas e de desempenho de rendimento semelhantes às da variedade elite, MR219. Duas linhas, PB-2-107 e PB-2-34, foram escolhidas como linhas potenciais por causa de seus desempenhos excelentes em comparação com a mãe, MR219. Este estudo demonstra uma história de sucesso de aplicação de MAS no desenvolvimento de linhas de arroz melhoradas com resistência a doenças contra a doença BLB.

Improvement of bacterial blight resistance of the high yielding, fine-grain, rice variety, Gangavati sona through marker-assisted backcross breeding.

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB.

Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.

High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133 cM across 16 linkage groups and 2169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

Pyramiding resistance genes for bacterial leaf blight (Xanthomonas oryzae pv. Oryzae) into the popular rice variety, Pratikshya through marker assisted backcrossing.

BACKGROUND: Bacterial leaf blight (BLB) is one of the major biotic stress in rice cultivation. Management techniques, such as the development of BLB-resistant cultivars, are required to lessen the severity of the disease attack and yield losses. Pratikshya was selected in the present investigation as the recipient parent, as it is one of the popular high-yielding rice varieties of Odisha, India, which is having excellent grain as well as cooking quality. However, Pratikshya is highly susceptible to BLB which is prevalent in Eastern Indian region. METHODS AND RESULTS: Three major BLB resistance genes xa5, xa13, and Xa21 from the donor source Swarna MAS (CR Dhan 800) were attempted to introduce into Pratikshya through a marker-assisted backcross breeding program. Those markers closely linked to the target genes were employed for foreground selection in the segregating generations till BC2F3. In each backcross generation, progenies containing all three targeted resistance genes and phenotypically more similar to the recipient parent, Pratikshya were selected and backcrossed. Screening of 1,598 plants of the BC2F2 population was conducted against BLB using Xoo inoculum and 35 resistant plants similar to Pratikshya were carried forward to the next generation. In the BC2F3 generation, 31 plants were found to possess all the three resistance genes. For background selection of plants carrying resistance genes 45 polymorphic SSR markers were employed. Evaluation of the pyramided lines at BC2F4 generation exhibited that, most pyramided lines were similar to Pratikshya in terms of morphological features and yield parameters, and some lines were superior to the recurrent parent in terms of morphological features and yield parameters. CONCLUSION: The three-gene pyramided lines showed a high level of resistance to BLB infection and are anticipated to offer a significant yield advantage over the recipient parent Pratikshya. The pyramided lines can further be used for multi-location trial, so as to be released as a variety or can be used as a potential donor for BLB resistance genes.

Backcrossing as a species restoration technique.

An investigation was conducted on the phenotypic results of mouse hybridization and seven generations of backcrossing, observing reciprocal F1 hybrids and backcrosses of Mus spretus and a laboratory strain of Mus domesticus C57BL/6J. F1 hybrids, backcrosses, and pure control specimens were measured for 6 body characteristics, 4 pelage coloration characteristics, 14 behaviors, and reproduction as reflected in litter size. Backcrossing was pursued for seven generations to FBC7 (i.e., "Backcross 7" or seven generations from commencement of backcrossing from an F1 hybrid female) where species restoration is mathematically calculated to be at 99.7%. Except for a minority of FBC7 M. spretus specimens failing to conform completely to one pelage characteristic, FBC7 specimens were indistinguishable from controls both subjectively and in all areas of measurement. The M. spretus backcross line was followed generation by generation and was largely conforming to controls by FBC4 at latest. The same effect was observed in the reciprocal M. domesticus backcross line. Fertility was negatively affected in F1 hybrids but restored or improved in backcross generations. Discussion is offered on hybridization and backcrossing as it occurs in nature and how it has been used or could be used as an additional ex situ tool in wildlife conservation efforts. It is concluded that conservation-oriented backcrossing is a practical species/subspecies restoration technique and has the potential to make genetic rescue feasible with minimal gene flow at the binomial level. Backcrossing is most applicable in closely monitored ex situ settings (1) where only one sex remains of a given taxon; and (2) where inbreeding depression seriously threatens a remnant taxon's ability to recover, and the only gene flow option is from another distinct species.

New insights into trait introgression with the look-ahead intercrossing strategy.

Trait introgression (TI) can be a time-consuming and costly task that typically requires multiple generations of backcrossing (BC). Usually, the aim is to introduce one or more alleles (e.g. QTLs) from a single donor into an elite recipient, both of which are fully inbred. This article studies the potential advantages of incorporating intercrossing (IC) into TI programs when compared with relying solely on the traditional BC framework. We simulate a TI breeding pipeline using 3 previously proposed selection strategies for the traditional BC scheme and 3 modified strategies that allow IC. Our proposed look-ahead intercrossing method (LAS-IC) combines look-ahead Monte Carlo simulations, intercrossing, and additional selection criteria to improve computational efficiency. We compared the efficiency of the 6 strategies across 5 levels of resource availability considering the generation when the major QTLs have been successfully introduced into the recipient and a desired background recovery rate reached. Simulations demonstrate that the inclusion of intercrossing in a TI program can substantially increase efficiency and the probability of success. The proposed LAS-IC provides the highest probability of success across the different scenarios using fewer resources compared with BC-only strategies.

Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea.

'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932.

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F1 plants. F1s were backcrossed with recurrent parent HD2932 to produce BC1F1 generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC1F1 and BC2F1 generations backcrossed and selfed to produce BC2F1and BC2F2 generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC1F1, BC2F1, and BC2F2 generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC2F2 generation and selfed to produce 27 BC2F3 NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

Improving Agricultural Traits While Maintaining High Resistant Starch Content in Rice.

BACKGROUND: Resistant starch (RS) is beneficial for human health. Loss of starch branching enzyme IIb (BEIIb) increases the proportion of amylopectin long chains, which greatly elevates the RS content. Although high RS content cereals are desired, an increase in RS content is often accompanied by a decrease in seed weight. To further increase the RS content, genes encoding active-type starch synthase (SS) IIa, which elongates amylopectin branches, and high expression-type granule-bound SSI (GBSSI), which synthesizes amylose, were introduced into the be2b mutant rice. This attempt increased the RS content, but further improvement of agricultural traits was required because of a mixture of indica and japonica rice phonotype, such as different grain sizes, flowering times, and seed shattering traits. In the present study, the high RS lines were backcrossed with an elite rice cultivar, and the starch properties of the resultant high-yielding RS lines were analyzed. RESULTS: The seed weight of high RS lines was greatly improved after backcrossing, increasing up to 190% compared with the seed weight before backcrossing. Amylopectin structure, gelatinization temperature, and RS content of high RS lines showed almost no change after backcrossing. High RS lines contained longer amylopectin branch chains than the wild type, and lines with active-type SSIIa contained a higher proportion of long amylopectin chains compared with the lines with less active-SSIIa, and thus showed higher gelatinization temperature. Although the RS content of rice varied with the cooking method, those of high RS lines remained high after backcrossing. The RS contents of cooked rice of high RS lines were high (27-35%), whereas that of the elite parental rice was considerably low (< 0.7%). The RS contents of lines with active-type SSIIa and high-level GBSSI expression in be2b or be2b ss3a background were higher than those of lines with less-active SSIIa. CONCLUSIONS: The present study revealed that backcrossing high RS rice lines with elite rice cultivars could increase the seed weight, without compromising the RS content. It is likely that backcrossing introduced loci enhancing seed length and width as well as loci promoting early flowering for ensuring an optimum temperature during RS biosynthesis.

Gene Editing to Accelerate Crop Breeding.

Recent advances in biotechnology have helped increase tissue transformation efficiency and the frequency and specificity of gene editing to an extent that introducing allelic variants directly in elite varieties has become possible. In comparison to the conventional approach of crossing an elite recipient line with an exotic donor parent to introduce the trait of interest followed by repeated backcrossing, direct introduction of major-effect allelic variants into elite varieties saves time and resources, and eliminates yield drag resulting from the residual donor genes at the end of backcrossing.

Effects of Various Allelic Combinations of Starch Biosynthetic Genes on the Properties of Endosperm Starch in Rice.

Rice endosperm accumulates large amounts of photosynthetic products as insoluble starch within amyloplasts by properly arranging structured, highly branched, large amylopectin molecules, thus avoiding osmotic imbalance. The amount and characteristics of starch directly influence the yield and quality of rice grains, which in turn influence their application and market value. Therefore, understanding how various allelic combinations of starch biosynthetic genes, with different expression levels, affect starch properties is important for the identification of targets for breeding new rice cultivars. Research over the past few decades has revealed the spatiotemporal expression patterns and allelic variants of starch biosynthetic genes, and enhanced our understanding of the specific roles and compensatory functions of individual isozymes of starch biosynthetic enzymes through biochemical analyses of purified enzymes and characterization of japonica rice mutants lacking these enzymes. Furthermore, it has been shown that starch biosynthetic enzymes can mutually and synergistically increase their activities by forming protein complexes. This review focuses on the more recent discoveries made in the last several years. Generation of single and double mutants and/or high-level expression of specific starch synthases (SSs) allowed us to better understand how the starch granule morphology is determined; how the complete absence of SSIIa affects starch structure; why the rice endosperm stores insoluble starch rather than soluble phytoglycogen; how to elevate amylose and resistant starch (RS) content to improve health benefits; and how SS isozymes mutually complement their activities. The introduction of active-type SSIIa and/or high-expression type GBSSI into ss3a ss4b, isa1, be2b, and ss3a be2b japonica rice mutants, with unique starch properties, and analyses of their starch properties are summarized in this review. High-level accumulation of RS is often accompanied by a reduction in grain yield as a trade-off. Backcrossing rice mutants with a high-yielding elite rice cultivar enabled the improvement of agricultural traits, while maintaining high RS levels. Designing starch structures for additional values, breeding and cultivating to increase yield will enable the development of a new type of rice starch that can be used in a wide variety of applications, and that can contribute to food and agricultural industries in the near future.

Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize.

BACKGROUND: Hybridization and backcrossing are commonly used in animal and plant breeding to induce heritable variation including epigenetic changes such as paramutation. However, the molecular basis for hybrid-induced epigenetic memory remains elusive. RESULTS: Here, we report that hybridization between the inbred parents B73 and Mo17 induces trans-acting hypermethylation and hypomethylation at thousands of loci; several hundreds (~ 3%) are transmitted through six backcrossing and three selfing generations. Notably, many transgenerational methylation patterns resemble epialleles of the nonrecurrent parent, despite > 99% of overall genomic loci are converted to the recurrent parent. These epialleles depend on 24-nt siRNAs, which are eliminated in the isogenic hybrid Mo17xB73:mop1-1 that is defective in siRNA biogenesis. This phenomenon resembles paramutation-like events and occurs in both intraspecific (Mo17xB73) and interspecific (W22xTeosinte) hybrid maize populations. Moreover, siRNA abundance and methylation levels of these epialleles can affect expression of their associated epigenes, many of which are related to stress responses. CONCLUSION: Divergent siRNAs between the hybridizing parents can induce trans-acting epialleles in the hybrids, while the induced epigenetic status is maintained for transgenerational inheritance during backcross and hybrid breeding, which alters epigene expression to enhance growth and adaptation. These genetic and epigenetic principles may apply broadly from plants to animals.

Over-expression in cis of the midgut P450 CYP392A16 contributes to abamectin resistance in Tetranychus urticae.

Cytochrome P450 mediated metabolism is a well-known mechanism of insecticide resistance. However, to what extent qualitative or quantitative changes are responsible for increased metabolism, is not well understood. Increased expression of P450 genes is most often reported, but the underlying regulatory mechanisms remain widely unclear. In this study, we investigate CYP392A16, a P450 from the polyphagous and major agricultural pest Tetranychus urticae. High expression levels of CYP392A16 and in vitro metabolism assays have previously associated this P450 with abamectin resistance. Here, we show that CYP392A16 is primarily localized in the midgut epithelial cells, as indicated by immunofluorescence analysis, a finding also supported by a comparison between feeding and contact toxicity bioassays. Silencing via RNAi of CYP392A16 in a highly resistant T. urticae population reduced insecticide resistance levels from 3400- to 1900- fold, compared to the susceptible reference strain. Marker-assisted backcrossing, using a single nucleotide polymorphism (SNP) found in the CYP392A16 allele from the resistant population, was subsequently performed to create congenic lines bearing this gene in a susceptible genetic background. Toxicity assays indicated that the allele derived from the resistant strain confers 3.6-fold abamectin resistance compared to the lines with susceptible genetic background. CYP392A16 is over-expressed at the same levels in these lines, pointing to cis-regulation of gene expression. In support of that, functional analysis of the putative promoter region from the resistant and susceptible parental strains revealed a higher reporter gene expression, confirming the presence of cis-acting regulatory mechanisms.

Evaluation of A3 cytoplasmic male sterile forage sorghum lines for resistance to sugarcane aphid.

MAIN CONCLUSION: Three known sugarcane aphid-resistant pollinator parents were sterilized in A3 cytoplasmic male sterility and were confirmed in this study to be resistant to sugarcane aphid allowing for the development of sugarcane aphid-resistant forage hybrids. We utilized A3 cytoplasmic male sterility and converted known sugarcane aphid-resistant sorghum TX 2783, and newly released R. LBK1 (Reg. No. GP-865, PI 687244) and R. LBK2 (Reg. No. GP-866, PI 687245) into A3 sterility to determine if the sterile counterparts would also equally express tolerance and or antibiosis to sugarcane aphid. Free-choice flat screen trials and life-table demographic studies were utilized and compared to know susceptible/fertile entries KS 585, and TX 7000, and known resistant/fertile entries TX 2783 and DKS 37-07. The R. LBK1 fertile entry was more tolerant than the known susceptible entries KS 585 and TX 7000, but was not as resistant as the other resistant entries, sustaining a damage rating of 6.0 across two different screen trials. The sterile A3 R. LBK2 showed a greater tolerance and expressed higher levels of antibiosis during aphid reproductive studies when compared to the known resistant and fertile TX 2783. All other fertile (R. LBK2, TX2783) and the A3 male sterile counterparts (A3 R. LBK2, A3 TX2783) were very similar in expression of high levels of tolerance and exhibited statistically similar damage ratings of 3.3-4.3 when exposed to sugarcane aphids. No entry, either fertile or sterile, was as tolerant as DKS 37-07, a known resistant commercial hybrid. Other plant measurements including percent loss in chlorophyll content, difference in plant height, and number of true leaves for sugarcane aphid infested versus non-infested were very consistent and highly correlated with damage ratings. Antibiosis was also exhibited in both fertile and sterile versions of the resistant lines. There was a 2 × reduction in fecundity between the R. LBK1 fertile and its sterile A3 R. LBK1 when compared to the susceptible KS 585 and TX 7000; however, the remaining fertile and sterile entries had 3.8 × to 5.8 × decrease in fecundity when compared to the susceptible KS 585 and TX 7000. Other measurements in life-table statistics such as nymphs produced/female/d, and the intrinsic rates of increased were significantly lower for all fertile and sterile lines, showing that antibiosis significantly affected sugarcane aphid reproduction. In conclusion, the A3 cytoplasmic male sterility shows consistency for maintaining the single dominant trait SCA-resistant trait of TX 2783 for expressing both antibiosis and tolerance, and great utility in the development of sugarcane aphid-resistant forage sorghums.

Pyramiding of genes for grain protein content, grain quality, and rust resistance in eleven Indian bread wheat cultivars: a multi-institutional effort.

Improvement of grain protein content (GPC), loaf volume, and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcross breeding (MABB) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24, and Sr24. GPC increased by 0.8 to 3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines allowed identification of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the backgrounds of the following four cultivars: NI5439, UP2338, UP2382, and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were obtained in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621, and DBW1. The improved pre-bred lines developed following multi-institutional effort should prove a valuable source for the development of cultivars with improved nutritional quality and rust resistance in the ongoing wheat breeding programmes. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01277-w.

An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂).

Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48, F1-F6) derived from distant hybridization between female Megalobrama amblycephala (BSB, 2n=48) and male Culter alburnus (TC, 2n=48), and the backcross progeny (BTB, 2n=48) derived by backcrossing female F1 of BT to male BSB, an improved hybrid bream (BTBB, 2n=48) was obtained by backcrossing BTB (♀) to BSB (♂). Moreover, the morphological and genetic characteristics of BTBB individuals were investigated; BTBB was similar to BSB in appearance but had a higher body height than BSB. The study results regarding chromosome numbers and DNA content indicated that BTBB is a diploid hybrid fish. The 5S rDNA and Hox gene of BTBB were inherited from the original parents. Gonadal development in BTBB was normal. On the other hand, BTBB had a faster growth rate, higher muscle protein level, and lower muscle carbohydrate level than BSB. Hence, bisexual fertile BTBB is promoted and can be applied as a high-quality fish, and it can also be used as a new fish germplasm resource to develop high-quality fish further. Thus, this study is of great significance for fish genetic breeding.