Eduardo Beche

Cacao ( Theobroma cacao L.) production is severely constrained by black pod rot (BPR) and frosty pod rot (FPR), two major diseases that cause substantial yield losses across the tropics. Breeding for disease resistance remains challenging due to long generation intervals and the complex genetic control of disease responses. Here, we used genome‐wide association studies (GWASs) and genomic prediction (GP) to dissect the genetic basis of BPR and FPR resistance in an interrelated multi‐parent F ₁ panel comprising 495 individuals derived from eight bi‐parental crosses. Whole‐genome sequencing of 495 F1 cacao plants yielded 103,479 high‐quality single‐nucleotide polymorphisms used for association mapping. GWAS identified 45 quantitative trait loci (QTLs) associated with BPR or FPR resistance, including a shared hotspot on chromosome 7 involved in both diseases. Disease resistance loci exhibited small individual effects (0%–8% variance explained), consistent with a highly polygenic architecture. Genomic prediction showed encouraging predictive abilities ranging from 0.36 to 0.64 for FPR and BPR. Multi‐trait GP models that incorporated secondary traits increased predictive ability between 1.3‐ and 2‐folds for frosty pod rot traits. Marker subset and training population analyses demonstrated that predictive ability plateaued at ∼1000 markers and ∼450 training individuals, respectively, with little improvements on accuracy after that. Our results highlight the polygenic nature of resistance to BPR and FPR and demonstrate the strong potential of incorporating secondary traits into a multi‐trait analyses for increasing accuracies for primary traits.

Crop core collections serve as a means of conserving genetic variation and providing a diverse array of accessions for future research and breeding endeavours. Despite the challenges posed by diseases and climate change to global cacao production, no centralized core collection currently exists. To address this gap, we have assembled a new, general-purpose cacao core collection from accessions present in international collections. A dataset of 310 cacao accessions from international collections were selected based on material availability, geographic origin, and known phenotypic characteristics. Population structure analysis of 26,601 single nucleotide polymorphisms (SNPs) from these accessions revealed ten distinct genetic groups, consistent with previous studies. A core collection of 96 accessions was subsequently selected, encompassing 99.6% of the genetic diversity within the dataset. This collection comprises representatives of all ten genetic groups, as well as accessions exhibiting high productivity and pathogen resistance. This core collection will serve as a crucial genetic resource for the cacao community. Cultivating and maintaining the plants from this core collection will contribute to the preservation of genetic diversity within the population. Furthermore, this collection, when combined with appropriate phenotyping, will establish a foundation for novel breeding programs aimed at enhancing crop improvement in the future.

In this study, the aim of this study was to identify the source of resistance using KASP markers developed for Rpp1 – Rpp5 and screening for resistance in field trials in F₂ populations. Ten F₂ soybean (Glycine max (L.) Merrill) populations derived from crosses between rust-susceptible (55I57RSF IPRO, 63I64RSF IPRO) and rust-resistant sources (PI 200492, PI 594538A, PI 587880A, PI 594723, PI 230970, PI 506764, PI 459025A and PI 200487) were evaluated. All F2 plants were individually evaluated in field conditions for ASR phenotypic reactions and classified according to sporulation level. KASP markers were developed according to assays associated with Rpp genes available at SoyBase. Based on a slight difference in map position and different phenotypic disease reactions of PI 200492, we suggest that PI 594723 carries a resistance gene Rpp1-b. The Rpp1-b gene from PI 594723 was mapped on Chr 18 in a 12.4 cM region. The PIs carrying Rpp1-b (PI 594723, PI 587880A, and 594538A) showed strong resistance to ASR compared to the lines carrying Rpp1 (PI 200492). A total of 26 KASP markers were significantly associated (P < 0.01) with ASR resistance. Among those, M1, M5, and M6 (Rpp1), M13 and M14 (Rpp2), M16, M17 and M20 (Rpp3), M25 and M26 (Rpp4), and M27 and M28 (Rpp5) have the potential to be used in marker-assisted selection strategies.

Pyramiding Rpp genes is a promising strategy to achieve a more durable resistance against Asian soybean rust (ASR). The objective of this study was to develop Rpp‐pyramided populations and evaluate their resistance and yield in field conditions. Fifteen pyramided populations carrying different combinations of Rpp genes were developed, and the F₃ lines were evaluated to phenotypic resistance and yield performance. Our results suggest that the Rpp1‐b of different resistant sources (PI 587880A, PI 594723, PI 4538A) have higher resistance and yield performance compared with other Rpp genes. Rpp‐pyramided populations carrying two and three genes showed an increase in resistance compared with populations carrying a single Rpp gene. The best gene combinations were Rpp1‐b + Rpp5, showing neither uredinia formation nor sporulation (immunity + RB1 phenotype reaction) in more than 70% of the F₃ population. Rpp‐pyramided lines developed in this study have the potential to be used in backcross programs for improving ASR resistance.

Glycine soja germplasm can be used to successfully introduce new alleles with the potential to add valuable new genetic diversity to the current elite soybean gene pool.

O objetivo deste trabalho foi caracterizar cultivares brasileiras de trigo, desenvolvidas em diferentes décadas, quanto à eficiência de uso de N, sob diferentes disponibilidades do nutriente. Dez cultivares de trigo, lançadas entre 1940 e 2009, foram submetidas a quatro doses de adubação nitrogenada (0, 60, 120 e 180 kg ha^-1 de N), em ambiente controlado, em delineamento de blocos ao acaso, com três repetições. A produtividade de grãos aumentou em 0,54, 0,74, 0,74 e 0,82% ao ano, nas doses de 0, 60, 120 e 180 kg ha^-1 de N, respectivamente. As eficiências de absorção e de utilização de N estiveram positivamente associadas à eficiência de uso do nitrogênio, com estreitamento na relação em condições de alta disponibilidade de N. As cultivares modernas são mais eficientes no uso do N e toleram doses mais baixas do nutriente, em comparação às cultivares pioneiras. Para o desenvolvimento de cultivares mais eficientes no uso de N, os programas de melhoramento genético de trigo devem priorizar a seleção de genótipos com maiores eficiências de absorção, remobilização e utilização de N.