Interest of phenomic prediction as an alternative to genomic prediction in grapevine

Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum reflects the biochemical composition within a tissue, under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been successfully applied in several cereal species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. We found that the co-inertia between spectra and genomic data was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, there was a correlation across traits between predictive ability of genomic and phenomic prediction, with a slope around 1 and an intercept of -0.2, thus suggesting that phenomic prediction could be applied for any trait.

Combining ability and heterotic value of ten lines maize genotypes tolerant to tidal-swamp soil stress

Development of maize hybrid for tidal swampland was initiated by selecting and combinate some superior line genotypes that tolerate to the restrictions in target environment. This study aimed was to evaluate the capability of ten maize lines result of selection on tidal swamp acid sulphate soils to obtain GCU, GCA, and heterosis values based on parental yield averages. The experiment has consisted of ten fine line genotypes which have selected in 2019 at the tidal swamp. Each parent was crossed in half-diallel combination, resulting in 46 entries, including the inbred parents. The entries were planted in a randomized complete block design with three replications. The research was conducted on Bajeng Research Station Experiment 5°18’S and 119°30’E from September 2020 to January 2021. The result shows that GCA ability and SCA ability was significant to yield in the form of grain (15% moisture content), the number of ear per plot, ten ear weight, ten corncob weight, ear harvested weight, 1000 seeds weight, plant height, ear length and the number of seed per ear. Grain yield of W6xW9 crosses obtains the highest value of 9.36 tha−1, non-significantly different to hybrid check P35 (9.35 tha-1). The highest GCA value in the grain yield character was obtained on W9 parental line (0.64**). The highest SCA was obtained on the crossing of W7 x W8 (2.61). The highest heterosis value was revealed in W5 x W10 hybrid (4.80). However, W7 x W8 crossing heterosis value was 2.34, indicate that a high SCA effect did not usually generate high heterosis. To perform high heterosis value, W10 was good as female parental.

Genetic Performance of Inbred and Hybrids of Maize Under Irrigation Interval

A field experiment was carried out using four inbred lines of maize BK112, Inb17, ZP607 and Zm6, as they were entered into half-diallel cross-breeding program in the fall season 2019, and 10 genotypes (6 crosses + 4 parents) were obtained according to the second Griffing method, the first model, in the spring season of 2020, the behavior of these inbreds and their hybrids were evaluated with three irrigation intervals with the aim of obtaining one or more distinct hybrids of pure strains derived from maize Zea mays L. under the irrigation interval and the study of hybrid vigor. The experiment was carried out in the fields of a farmer in Anbar Governorate, using the RCBD randomized complete block design (split – plot) with three replications. The irrigation interval (4, 8 and 12) days occupied the main plots, while the inbred and hybrids occupied the sub-plots. The results of the statistical analysis showed a significant effect of genotypes on the studied traits. The studied hybrids Zm6 × ZP607 were distinguished by their weight of 300 grains and the grain yield (85.83 g and 186.70 g) respectively. The plants grown under the irrigation interval 4 days outperformed the grain yield of the plant by giving it the highest yield of 156.03 g. It did not differ significantly with the 8-day irrigation interval, while the yield decreased significantly at the 12-day irrigation interval with a decrease of 120.8% and 120.5% than the 4 and 8 irrigation treatments, respectively. It was also found that the interaction was significant and reached the highest grain yield with an irrigation interval of 8 days, 224.0 g. The hybrid Zm6 × ZP607 gave the highest positive hybrid vigor for individual plant yield, which was 119.24%, 126.72% and 166.05% for the irrigation interval of 4, 8 and 12 days, respectively. Therefore, the plant breeder can use the characteristics of the yield components as selection guides with the superior hybrids in yield and the strength of the hybrid.

Combining ability analysis of maize lines under optimal and low nitrogen stress

Most of the land for maize development in Indonesia has low N limiting factor, thus it is necessary to develop a proper maize breeding programs tolerant to low N conditions. One of the breeding methods suitable for low N evaluation is the diallel method between inbred parents (homozygous lines) that are tolerant of low N stress. The aim of this study was to assess the genotype tolerance to low N with comparable yields. The research consisted of two stages. The first stage is the development of hybrid maize grains (F1) using the half diallel cross method. This activity was carried out in KP. Maros, Research Center for Cereal Crops. A half-diallel cross refers to the Griffing IV method, by involving 11 low N-tolerant genotypes (AVLN 100-1, AVLN 118-2, AVLN 122-2, AVLN 124-4, AVLN 32-3, AVLN 83-1, AVLN 83-4, AVLN 83-6, AVLN 86-2, MAL 04, and AVLN 124-9). The second stage was carried out in KP. Bajeng to evaluate 52 genotypes of hybrid maize from diallel crosses plus four hybrid varieties Advanta 777, Bisi 18, P 27 and JH 37 for control. The experiment was carried out under conditions of low N stress (100 kg N/ha) and normal N (200 kg N/ha). The experiment used a randomized block design with three replications. Hybrids that are tolerant (T) under conditions of low N stress was best indicated by AVLN 83-4/AVLN 124-4 genotype pair, with significant higher grain yield than Bisi-18 and JH 37 varieties. This hybrid produced average grain yield of 7.87 t/ha under both conditions. Inbred maize genotypes classified as medium tolerant (MT) were AVLN 83-4/AVLN 124-9, AVLN 124-4/AVLN 86-2, AVLN 122-2/AVLN 124-4, AVLN 83-1/AVLN 124-9, has similar yield potential as to the control varieties.

Parents’ Performance and F1 Crosses For Several Bread Wheat Cultivars Under Varying Levels of Nitrogen Fertilization

Six bread wheat varieties representing different traits were crossed in a half-diallel in 2017/2018 season. The 6 parents and its 15 F1 crosses were evaluated under normal and N-stress conditions in 2018/2019 season, to study the mean performance and the combining ability for earliness and morpho-physiological traits and biomass yield of wheat under normal and N-stress conditions. Mean squares of genotypes, parents, crosses, and parents versus crosses were significant or highly significant for most of the studied traits and biological yield under both conditions, reflecting a sort of heterosis for these characters. Mean squares of GCA and SCA were significant or highly significant for most of the studied traits under both conditions, indicating the presence of both additive and non-additive types of genes in the genetic system controlling these traits. The best general combiners were P1 (Giza 168) and P2 (Sakha 94) at both conditions, P3 (Shandweel 1) at N-stress, and P4 (Gemmeiza 11) at normal condition for earliness and P6 (Misr 1) at both conditions and P5 (Sids 12) at N-stress and P3 (Shandweel 1) at normal condition for biomass yield plant-1. The best cross combinations were crosses No.3 (P1xP4), No.5 (P1xP6), No.6 (P2xP3), No.7 (P1xP2), No.8 (P2xP5) and No.11 (P3xP5) under N-stress for earliness; and crosses No.3 (P1xP4), No.7 (P2xP4), No.8 (P2xP5), No.12 (P3xP6), No.14 (P4xP6) and No.15 (P5xP6) at both conditions, and cross No.2 (P1xP3) under N-stress for biomass yield plant-1.

Parental Diversity and Its Relationship with Performance of F1 Hybrid in Rice (Oryza sativa L.)

The present investigation was carried out including 10 parents and their 45 half diallel crosses with the objective to study the relationship between heterosis and diverse genotype. The Mahalonobis D2values resulted in grouping of 10 parents into 3 clusters. Cluster I was comprised of four genotypes, cluster II comprised of five genotypes while, cluster III was found monogenotypic. Cluster II and Cluster III had maximum mean values for 4 traits. Highest intercluster distance was also observed in these 2 cluster followed by cluster I and III . Maximum intra cluster distance was observed in cluster II followed by cluster I. The highest contribution in the manifestation of total genetic divergence was exhibited by grain iron content followed by grain zinc content. The relationship between parental diversity and heterosis indicated that majority of crosses belong to moderate divergence class. The cross P4×P5 exhibiting better parent heterosis for maximum traits also exhibited at par mean performance for 5 traits including grain yield per plant over the better parent. For grain zinc content, two crosses from high and low while, nine crosses from moderate divergence classes reported positive significant heterosis and SCA effects. For grain iron content, 1 cross with high, 2 crosses with moderate while four crosses with low divergence classes reported significantly positive heterosis and SCA effects.

Half Diallel Analysis for Biochemical and Morphological Traits in Cultivated Eggplants (Solanum melongena L.)

Eleven morphologically diverse cultivated eggplant accessions were used for hybridization following half diallel mating design to obtain 55 hybrids. Evaluation of hybrids along with the parents was conducted over two locations followed by randomised complete block design with three replications to study gene action and combining ability of 15 morphological and biochemical traits. The analysis of variance indicated highly significant differences among the environments and interaction of genotype and environment, except for fruit length to width ratio. Additive gene effects were significant for the inheritance of these traits and expression of these additive genes were greatly affected by environments. The general combining ability (GCA) was greater than their respective specific combining ability (SCA) for all traits except for fruit yield per plant. High values of GCA and SCA effects for characters of interest were dispersed among different genotypes. From this study it was observed that the best parental line was BT15 based on days to first flowering, total number of fruits per plant, total soluble solids and total phenol content. Besides, the parent BM5 showed good general combining ability effects for fruit yield per plant, fruit length and fruit length to width ratio and the parent BB1 performed good general combining ability for fruit diameter, fruit girth and fruit weight. Besides, other parents showed the best performance for only one trait. On the other hand, the hybrid BT6 × BT15 was reported bearing early flowering with high total phenol content and the hybrid BM9 × BB26 has high fruit yield with high soluble solids. Besides, the hybrid BM9 × BB1 has a high fruit diameter and fruit weight. All other hybrids except for these three (BT6 × BT15, BM9 × BB26 and BM9 × BB1) were shown the best performance for only one trait. Hence, based on the desired trait, the hybrid can be selected for future use after large scale evaluation.

QTL Mapping in Outbred Tetraploid (and Diploid) Diallel Populations

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multi-allelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and non-additive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with 3 tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.