Haploid Lines Research Articles

Quantitative Trait Loci Mapping for Powdery Mildew Resistance in Wheat Genetic Population

Background/Objectives: Powdery mildew is a prevalent wheat disease that affects yield and quality. The characterization and fine mapping of genes associated with powdery mildew resistance can benefit marker-assisted breeding. Methods: In this study, quantitative trait loci (QTL) associated with powdery mildew were mapped using a high-density 35K DArT genetic linkage map developed from a population of double haploid lines (DHs) created by crossing “Jinmai 33 (a highly resistance line) with Yannong 19 (a highly susceptible line)”. Results: Three stable QTLs for powdery mildew were identified on chromosomes 1B, 2B, and 6A combined with the composite interval graphing method and multiple interval mapping, explaining phenotypic variations (PVE) that range from 4.98% to 13.25%. Notably, Qpm.sxn-1B and Qpm.sxn-2B were identified across three environments, with the PVE ranging from 9.37% to 13.25% and from 4.98% to 5.23%, respectively. The synergistic effects of these QTLs were contributed by the parental line “Jinmai 33”. Qpm.sxn-1B was the major stable QTL, and Qpm.sxn-2B was close to Pm51. Furthermore, Qpm.sxn-6A was identified in two environments, accounting for PVE values of 7.13% and 7.65%, respectively, with the resistance effects originating from the male parent. Remarkably, this locus has not been reported previously, indicating that Qpm.sxn-6A represents a newly dis-covered QTL governing powdery mildew genes. Conclusions: Five molecular markers available for mark-er-assisted selection were selected for tracking Qpm.sxn-1B and Qpm.sxn-2B in the program. The identification of this novel newly discovered QTL and markers reported in this study will be useful for marker-assisted selection of powdery mildew resistance.

Agronomic Performance and Resistance to Maize Lethal Necrosis in Maize Hybrids Derived from Doubled Haploid Lines

Maize (Zea mays L.) is one of the most widely cultivated grain crops globally. In sub-Saharan Africa (SSA), it plays an important role in ensuring both food and income security for smallholder farmers. This study was conducted to (i) assess the performances of testcross hybrids constituted from maize lethal necrosis (MLN) tolerant doubled haploid (DH) lines under various management conditions; (ii) estimate the combining ability effects and determine the nature of gene action in the DH lines; and (iii) identify DH lines and testcross hybrids for resistance to MLN, high grain yield, and other important traits. Eleven DH lines were crossed with 11 single-cross testers using the line-by-tester mating design, and 115 successful testcross hybrids were generated. These hybrids, along with five commercial check hybrids, were evaluated across four optimum management conditions, two MLN artificial inoculations, and one managed drought environment in Kenya. Under each management condition, the effects of genotypes, environments, and genotype-by-environment interactions were significant for grain yield (GY) and most other traits. Hybrids T1/L3, T10/L3, and T11/L3 exhibited higher grain yields under at least two management conditions. A combining ability analysis revealed that additive gene effects were more important than non-additive effects for GY and most other traits, except for leaf senescence (SEN) and MLN disease severity score. DH line L3 exhibited a desirable general combining ability (GCA) effect for GY, while L5 was the best general combiner for anthesis date (AD) and plant height (PH) across all management conditions. DH lines L2, L6, and L7 showed negative GCA effects for MLN disease severity. Single-cross testers T11 and T10 were good general combiners for GY under all management conditions. Hybrids T2/L11, T9/L10, and T2/L10 demonstrated high specific combining ability (SCA) effects for GY under all conditions. This study identified DH lines and testers with favorable GCA effects for grain yield, MLN resistance, and other agronomic traits that can be used in breeding programs to develop high-yielding and MLN-resistant maize varieties. Better-performing testcross hybrids identified in the current study could be verified through on-farm testing and released for commercial production to replace MLN-susceptible, low-yield hybrids grown in the target ecologies.

Doubled Haploid Technology: Generation of Doubled Haploid Maize Lines Using Haploid Inducers.

Doubled haploid (DH) technology allows for the development of completely homozygous lines from heterozygous plants in only two generations. This approach has been widely adopted in maize breeding programs, as it expedites the generation of inbred lines compared to traditional methods. The DH approach is based on the use of maize genotypes that have the ability to induce haploid seeds when used as the pollen parent. The most common method for producing maize haploid plants for the generation of DH lines is in vivo maternal haploid induction. The process involves pollination with a haploid inducer maize line to generate haploid seeds. Then, haploids are screened for and identified (typically via the expression of a particular marker gene), germinated, treated with an exogenous doubling agent to induce genome duplication, and transplanted to the field. Following successful self-pollination, seeds harvested from the ear represent fully homozygous lines. The seed set at this stage, however, is often low, necessitating one or two additional rounds of self-pollination to increase the number of fully homozygous inbred lines. Here, we describe a protocol for the generation of maize DH lines using maternal haploid-inducing maize lines. We outline the steps for setting up the donor material, performing induction crosses, selecting haploids based on two different marker alleles, treating seedlings with colchicine to double the genome, transplanting the treated seedlings to the field, and self-pollinating the treated plants.

Impact of genotype × environment interaction and selection history on genomic prediction in maize (Zea mays L.)

AbstractBreeders made remarkable progress in improving productivity and stability of cultivars. Breeding progress relies on selecting favorable alleles for performance and stability to produce productive varieties across diverse environments. In this study, we analyzed the Genomes to Fields Initiative 2018–2019 genotype by environment interaction (G × E) dataset, focusing on three populations of double haploid (DH) lines derived from crossing inbrexpired Plant Variety Protection (ex‐PVP) inbred line PHW65 with inbred lines PHN11, Mo44, and MoG. PHW65 is an Iodent/Lancaster‐type inbred; PHN11 is an Iodent type ex‐PVP line; Mo44 is a tropical‐derived inbred; and MoG is an agronomically poor line derived from the variety Mastadon. Hybrids were produced by crossing the resulting DHs with Stiff Stalk testers PHT69 and LH195. The study's objective was to determine the donor inbreds' relative value and understand the impact of selection history on genomic prediction. We conducted a two‐stage analysis to compare hybrid performance and G × E variance of the populations. G × E variance for yield was significantly lower in the PHW65 × PHN11 population relative to the PHW65 × MoG population. The reduced G × E variance of the PHN11 population led to increased indirect prediction accuracy (when training and testing data are drawn from the same population but different environments). In cross‐validation, the PHN11 population had the greatest indirect prediction accuracy 45% of the time, followed by the Mo44 population (30%) and the MoG population (25%). Results demonstrate that prediction accuracy was greater in the population with the longest history of selection for favorable alleles (PHN11), contributing to greater yield stability.

Development of Haploid Plants by Shed-Microspore Culture in Platycodon grandiflorum (Jacq.) A. DC.

Anther and microspore cultures are efficient methods for inducing haploids in plants. The microspore culture by chromosome-doubling method can produce double haploid lines, developing pure lines within the first or second generations. This study aimed to induce haploid plants in Platycodon grandiflorum using the shed-microspore culture method. P. grandiflorum floral buds (n = 1503) were cultured in six types of medium to induce haploids. Anthers were placed on a solid-liquid double-layer medium and cold pre-treated at 9 °C for one week, followed by incubation in the dark at 25 °C. Embryogenesis was observed after approximately 70 days of culture, producing haploid plants through regeneration. Of the 1503 floral buds, embryos developed in 120 buds, resulting in the induction of 402 individuals. Among the media used, Schenk and Hildebrandt (SH) and 1/2SH exhibited high efficiency, with embryogenesis ratios of 12% and 13.4%, respectively. Additionally, the highest embryogenesis ratio (15.3%) was observed in flower buds sized 10 mm or less. Therefore, we established shed-microspore culture conditions to induce haploids in P. grandiflorum. Using this method, haploids can be efficiently induced in P. grandiflorum, shortening the breeding period by enabling the rapid development of inbred lines.

CRISPR/Cas9 and Anther Culture for Precision Double Haploid Line Production in Controlled Environments

ABSTRACTThe development of mapping populations and quantitative trait loci (QTL) analysis face constraints, in crops exhibiting male sterility and self‐incompatibility under field conditions. Addressing these challenges requires the integration of advanced techniques, including the temporal alteration or excision of centromere histone H3 (CENH3) protein and the use of gene editing tools such as MATRILINEAL (MTL) knockout. Specifically, this can be achieved through Cas9/gRNA‐mediated mutagenesis or Cas9/gRNA‐driven promoter expression systems. These technologies offer efficient means to advance mapping populations and QTL analysis in male sterile and self‐incompatible crops within controlled ecosystems. The doubled haploid (DH) mapping population, traditionally requiring 3 years of generation time via anther culture method, can now be expedited to 2–3 years of generation time using gene editing techniques within controlled environmental systems. Notably, DH mapping populations can be efficiently generated in various crops, including rice, wheat, maize, barley and oats by leveraging gene editing tools. Among these tools, the novel approach of CENH3 protein temporal alteration/excision emerges as highly efficient compared to MTL knockout using Cas9/gRNA‐mediated mutation or Cas9/gRNA promoter expression. However, further investigation is warranted to optimise the regeneration of double haploid populations and enhance QTL analysis in male sterile and self‐incompatible crops under controlled systems.

Insights into the molecular basis of beet curly top resistance in sugar beet through a transcriptomic approach at the early stage of symptom development

Curly top disease caused by Beet curly top virus (BCTV) is a limiting factor for sugar beet production. The most economical and sustainable control of BCTV in sugar beet would be via the growth of resistant cultivars, although most commercial cultivars possess only low-to-moderate quantitative resistance. A double haploid line (KDH13) showed a high level of resistance to BCTV infection. However, the mechanism of resistance and response of this line to BCTV infection is unknown. Here, we tested the response of this line to both local and systemic BCTV infections. The virus replicated at a high level in locally infected tissue but lower than in susceptible KDH19 plants. Resistant KDH13 plants systemically infected with BCTV showed only mild enation without leaf curling after 30 days. In contrast, severe leaf curling appeared after 12 days in susceptible plants with higher virus accumulation. Transcriptome analysis of the BCTV-infected KDH13 plants at the early stage of symptom development showed only 132 genes that were exclusively deregulated compared to the regulation of a large number of genes (1018 genes) in KDH19 plants. Pathway enrichment analysis showed that differentially expressed genes were predominantly involved in hormone metabolism, DNA methylation, immune response, cell cycle, biotic stress and oxidative stress. The auxin level in both resistant and susceptible plants increased in response to BCTV infection. Remarkably, exogenous application of auxin caused leaf curling phenotype in the absence of the virus. This study demonstrates the response of resistant and susceptible plants to BCTV infection at both local and systemic infections and highlights the defence-related genes and metabolic pathways including auxin for their contribution towards BCTV symptom development and resistance in sugar beet.

Accelerated development of maize inbred lines suitable for high density through doubled haploid technology

Aim: Doubled haploid technology was utilized to accelerate the development of maize lines with traits suitable for high planting density, enabling the identification of potential parental lines for hybrid development under these conditions. Methodology: Two F1 populations (PML-119 x PML-185 and PML-95 x PML-172) were used to generate doubled haploid lines, confirmed using polymorphic markers phi115 and umc1887. These lines were phenotypically evaluated under high density (60 cm x 15 cm) and normal density (60 cm x 20 cm) conditions. Results: Using doubled haploid technology, 67 lines were developed from two source populations with traits such as narrow leaf angle, moderate plant height, and sparse tassel for high planting density stress tolerance. Molecular marker screening confirmed the homozygosity of these lines. Agronomic evaluation under narrow plant-to-plant spacing (15 cm) identified eight potential donor lines amenable to high planting density stress, ready for use as parents in breeding high-density tolerant hybrids. Interpretation: Potential donor doubled haploid lines viz. DH2-4, DH2-8, DH2-9, DH2-11, DH2-14, DH2-15 derived from Population-3 X CIM2GTAIL P2 and DH2-4, DH2-23 derived from Population-9 X CIM2GTAIL P2 were identified for utilization as putative parents of hybrids suitable for planting under high planting density conditions. Key words: Doubled haploid, High plant density, Maize, Plant architecture, Yield

Resistance of Doubled Haploid Rice Lines with Green Super Rice Characters to Bacterial Leaf Blight

<p>Bacterial leaf blight (BLB), caused by <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> (<em>Xoo</em>) is a significant disease attacking rice crops worldwide. This disease attacks at various stages of plant growth and causes significant yield loss. Breeding new varieties resistant to BLB is important to support sustainable agriculture in the future. This study aimed to identify new superior green super rice (GSR) lines resistant to BLB disease. The experiment evaluated the resistance of lowland rice lines obtained from anther culture using a factorial randomized complete block design. The 1<sup>st</sup> factor was genotype, consisting of 20 lines, 2 checks of commercial varieties (Inpari 42 Agritan GSR and Inpari 18), a resistant check (Conde), and a susceptible check (Taichung Native 1). The 2<sup>nd</sup> factor was BLB pathotypes (i.e., III, IV, and VIII). Quantitative data on disease severity and severity index were analyzed using analysis of variance and t-Dunnett test at 5% level. The results showed that the interaction between genotype and pathotype affected the disease severity and severity index in both growth phases. The tested lines exhibited varying resistance, from susceptible to resistant, to BLB. Four lines (SN 11, 13, 57, and 58) showed moderate to resistant criteria for BLB disease of 3 pathotypes in both growth phases. The selected lines can be used as a source of parents for breeders and candidates for new superior varieties with BLB resistance properties to support the reduction of synthetic chemical bactericide inputs and control BLB disease. However, further field evaluations are necessary to assess their performance.</p>

Haploid induction: an overview of parental factor manipulation during seed formation.

In plants, in vivo haploid induction has gained increasing attention for its significant potential applications in crop breeding and genetic research. This strategy reduces the chromosome number in progeny after fertilization, enabling the rapid production of homozygous plants through double haploidization, contrasting with traditional inbreeding over successive generations. Haploidy typically initiates at the onset of seed development, with several key genes identified as paternal or maternal factors that play critical roles during meiosis, fertilization, gamete communication, and chromosome integrity maintenance. The insights gained have led to the development of efficient haploid inducer lines. However, the molecular and genetic mechanisms underlying these factors vary considerably, making it challenging to create broadly applicable haploidy induction systems for plants. In this minireview, we summarize recent discoveries and advances in paternal and maternal haploid induction factors, examining their current understanding and functionalities to further develop efficient haploid inducer systems through the application of parental factor manipulation.

QTL mapping of maize plant height based on a population of doubled haploid lines using UAV LiDAR high-throughput phenotyping data

Maize (Zea mays L.) is a globally significant crop that plays a crucial role in feeding the growing global population. Among its various traits, plant height is particularly important as it affects yield, lodging resistance, ecological adaptability, and other important factors. Traditional methods for measuring plant height often lack cost-efficiency and accuracy. In this study, we employed a light detection and ranging (LiDAR) sensor mounted on an unmanned aerial vehicle (UAV) to collect point cloud data from 270 doubled haploid (DH) lines. This innovative application of UAV-based LiDAR technology was explored for high-throughput phenotyping in maize breeding. We constructed high-density genetic maps and assessed plant height at both single-plant and row scales across multiple developmental stages and genetic backgrounds. Our findings revealed that for many varieties and small areas, single-plant-scale estimation accuracy was superior to row-scale estimation, with an R2 of 0.67 versus 0.56 and an RMSE of 0.12 m vs. 0.17 m, respectively. Two high-density genetic maps were constructed based on SNP markers. In Sanya and Xinxiang, the F1DH and F2DH populations identified 12 and 20 QTLs (quantitative trait loci) for plant height, respectively. The study successfully identified and validated QTLs associated with plant height, revealing novel genetic loci and candidate genes. This research highlights the potential of UAV-based remote sensing to advance precision agriculture by enabling efficient, large-scale phenotyping and gene discovery in maize breeding programs.

Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.

The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of two future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSV) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes which enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in four generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level which was obtained by means of simulation for the "corn" and "cattle" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study.

Application of mannitol as pre-treatment and sucrose supports callus induction through anther culture in Gossypium arboreum

Diploid or tree cotton (Gossypium arboreum) species may provide a breeding source for fiber quality and disease resistance. Developing homozygous lines of Gossypium arboreum through anther culture can be a successful strategy for breeding the parental lines needed for cotton hybrids. This study describes callus induction on four G. arboreum genoytypes under various concentrations of sucrose as well as plant growth regulators. Explant materials were derived from immature anther and grew on modified Murashige and Skoog (MS) media. Prior to main treatment, mannitol application were applied to anthers with concentration of 0.7 M and modified MS media consisted of 3%, 5%, and 7% sucrose, as well as an addition of IAA, NAA, BAP, 2,4-D and Kin. Optimum callus formation was observed in Marvi genotype, in a medium containg IAA as well as sucrose between 5-7%. Furthermore, combination of IAA and NAA with sucrose 7% indicates highest number of embryogenic calli. However, Marvi genotype showed decreased rate of callus formation when the amount of sucrose increased on MS supplemented with NAA medium. The results indicated that the best formula on each genotypes were different. However, MS media with IAA (1 mg/l) + kin (0.2 mg/l) + CM (70 ml/l) + sucrose 5% provided the best performance to produce embryogenic calli on each genotypes. Our report can be utilized as an opportunity and strategy to obtain double haploid lines as a parental source in hybrid production.

Genomic prediction of the performance of tropical doubled haploid maize lines under artificial Striga hermonthica (Del.) Benth. infestation.

Striga hermonthica (Del.) Benth., a parasitic weed, causes substantial yield losses in maize production in sub-Saharan Africa. Breeding for Striga resistance in maize is constrained by limited genetic diversity for Striga resistance within the elite germplasm and phenotyping capacity under artificial Striga infestation. Genomics-enabled approaches have the potential to accelerate identification of Striga resistant lines for hybrid development. The objectives of this study were to evaluate the accuracy of genomic selection for traits associated with Striga resistance and grain yield (GY) and to predict genetic values of tested and untested doubled haploid maize lines. We genotyped 606 doubled haploid lines with 8,439 rAmpSeq markers. A training set of 116 doubled haploid lines crossed to 2 testers was phenotyped under artificial Striga infestation at 3 locations in Kenya. Heritability for Striga resistance parameters ranged from 0.38-0.65 while that for GY was 0.54. The prediction accuracies for Striga resistance-associated traits across locations, as determined by cross-validation (CV) were 0.24-0.53 for CV0 and from 0.20 to 0.37 for CV2. For GY, the prediction accuracies were 0.59 and 0.56 for CV0 and CV2, respectively. The results revealed 300 doubled haploid lines with desirable genomic estimated breeding values for reduced number of emerged Striga plants (STR) at 8, 10, and 12 weeks after planting. The genomic estimated breeding values of doubled haploid lines for Striga resistance-associated traits in the training and testing sets were similar in magnitude. These results highlight the potential application of genomic selection in breeding for Striga resistance in maize. The integration of genomic-assisted strategies and doubled haploid technology for line development coupled with forward breeding for major adaptive traits will enhance genetic gains in breeding for Striga resistance in maize.

Modeling the impact of resource allocation decisions on genomic prediction using maize multi‐environment data

AbstractIn a hybrid maize (Zea mays L.) breeding program that utilizes genomic selection, resource allocation used in phenotypic data acquisition must be balanced between population size, number of environments, and the number of testers used for generating hybrids. Plant breeders evaluate newly developed inbred lines using multi‐environment trials to account for genotype‐by‐environment interaction effects. The replication of hybrids across environments in these trials impacts the training data accuracy for developing genomic prediction models. This study examined the impact of resource allocation scenarios on genomic prediction accuracy using a multi‐environment trial dataset generated using inbred lines crossed to multiple testers. A total of 369 Stiff Stalk double haploid lines from a synthetic mapping population were testcrossed to three non‐Stiff Stalk inbred lines as testers, PHZ51, PHK76, and PHP02, and evaluated across 34 environments by the Genomes to Fields Initiative in 2020 and 2021. Resource allocation scenarios significantly impacted site‐specific genomic prediction accuracy for unobserved hybrids in unobserved environments. A training set with three to five environments that had the highest quality data produced similar prediction accuracy as data from 10 random environments for both observed and unobserved hybrids, indicating that strong prediction models can be built with a limited set of environments for both grain yield and plant height. We found that resource‐efficient prediction models that use data from one tester and three to five environments can effectively conduct selection of untested hybrids and in untested environments. Public research programs are often limited in testing capacity, and this study provides support for genomic selection in resource‐limited breeding programs.

In vivo haploid induction in cauliflower, kale, and broccoli.

Modifying the centromeric histone CENH3 or PHOSPHOLIPASE D genes in cauliflower (Brassica oleracea var. botrytis) created haploid induction lines, which can be widely used for in vivo haploid induction in cauliflower, kale, and broccoli, thus enabling rapid utilization of germplasm resources and improving breeding efficiency.

Determining arsenic stress tolerance genes in rice (Oryza sativa L.) via genomic insights and QTL mapping with double haploid lines

Arsenic, a hazardous heavy metal with potent carcinogenic properties, significantly affects key rice-producing regions worldwide. In this study, we present a quantitative trait locus (QTL) mapping investigation designed to identify candidate genes responsible for conferring tolerance to arsenic toxicity in rice (Oryza sativa L.) during the seedling stage. This study identified 17 QTLs on different chromosomes, including qCHC-1 and qCHC-3 on chromosome 1 and 3 related to chlorophyll content and qRFW-12 on chromosome 12 related to root fresh weight. Gene expression analysis revealed eight candidate genes exhibited significant upregulation in the resistant lines, OsGRL1, OsDjB1, OsZIP2, OsMATE12, OsTRX29, OsMADS33, OsABCG29, and OsENODL24. These genes display sequence alignment and phylogenetic tree similarities with other species and engaging in protein-protein interactions with significant proteins. Advanced gene-editing techniques such as CRISPR-Cas9 to precisely target and modify the candidate genes responsible for arsenic tolerance will be explore. This approach may expedite the development of arsenic-resistant rice cultivars, which are essential for ensuring food security in regions affected by arsenic-contaminated soil and water.

Development of double haploid lines using anther culture method with different F2 combinations

Development of double haploid lines using anther culture method with different F2 combinations

Breeding for Resistance to Biotic Stresses in Crops: Conventional to Genome Editing

Biotic stress is caused by fungi, bacteria, viruses, insects, nematodes as well weeds and it significantly reduces crop yield globally. For instance, the outbreak of a new strain of stripe rust in wheat worldwide, the emergence of white scale insect affecting mango in Ethiopia, the newly emerged Maize Lethal Necrosis viral disease in maize, and invasive fall armyworm insect are devastating maize crop and causing yield loss in Africa. To reduce the yield losses due to biotic stresses, the development of resistant variety and integrated insect pest approach is the way forward for managing disease and insects at respective agroecologies. Thus, this review paper discussed on conventional breeding methods and molecular-assisted selection for breeding resistance to foliar disease in major cereal crops. Wide array of germplasm such as landraces, recombinant inbred lines, pure lines, Double haploid lines, elite lines, multi-parent population, mutant lines, introgressed lines, hybrids, open population variety and wild relative can be used as source germplasm and should be screened under artificial inoculation and or at hotspot areas to develop disease resistance variety. Many maize inbred lines and hybrids showed resistance to turcicum leaf blight, grey leaf spot and common rust diseases and indicating that these genotypes have carrying genes/favorable alleles for multiple disease resistance and it is possible to develop variety resistance to fungi foliar disease in maize. Similarly, several advanced lines and some varieties showed resistance to strip and leaf rust in wheat. However, host plant resistance could be broken down due to new emerging race pathogens. Thus, conventional breeding and molecular screening should be integrated for resistant variety development. Indeed, Marker-assisted selection through backcrossing, gene pyramiding, combined Genome-Wide Association, and transcriptome approach is useful to identify candidate genes and resistant parents in crops. .......

Optimising desired gain indices to maximise selection response.

In plant breeding, we often aim to improve multiple traits at once. However, without knowing the economic value of each trait, it is hard to decide which traits to focus on. This is where "desired gain selection indices" come in handy, which can yield optimal gains in each trait based on the breeder's prioritisation of desired improvements when economic weights are not available. However, they lack the ability to maximise the selection response and determine the correlation between the index and net genetic merit. Here, we report the development of an iterative desired gain selection index method that optimises the sampling of the desired gain values to achieve a targeted or a user-specified selection response for multiple traits. This targeted selection response can be constrained or unconstrained for either a subset or all the studied traits. We tested the method using genomic estimated breeding values (GEBVs) for seven traits in a bread wheat (Triticum aestivum) reference breeding population comprising 3,331 lines and achieved prediction accuracies ranging between 0.29 and 0.47 across the seven traits. The indices were validated using 3,005 double haploid lines that were derived from crosses between parents selected from the reference population. We tested three user-specified response scenarios: a constrained equal weight (INDEX1), a constrained yield dominant weight (INDEX2), and an unconstrained weight (INDEX3). Our method achieved an equivalent response to the user-specified selection response when constraining a set of traits, and this response was much better than the response of the traditional desired gain selection indices method without iteration. Interestingly, when using unconstrained weight, our iterative method maximised the selection response and shifted the average GEBVs of the selection candidates towards the desired direction. Our results show that the method is an optimal choice not only when economic weights are unavailable, but also when constraining the selection response is an unfavourable option.