The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color

Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.

Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach

Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.

Perbedaan pertumbuhan dan produktivitas varietas bayam hijau dan bayam merah

Bayam termasuk salah satu sayuran terpenting di Indonesia karena paling banyak dikonsumsi setelah kangkung. Bayam hijau dan bayam merah merupakan jenis bayam paling banyak ditanam dan dikonsumsi. Penelitian ini bertujuan untuk mengetahui perbedaan pertumbuhan dan produktivitas varietas bayam hijau dan bayam merah. Penelitian dilakukan pada Februari – April 2021 di Kebun Percobaan Leuwikopo, Departemen Agronomi dan Hortikultura, Fakultas Pertanian, IPB University. Sebanyak 9 varietas bayam hijau (Maryland, Richie, Maestro, Benua, Doly, Khanafiah, Manila, Pacific, White Leaf) dan 4 varietas bayam merah (Mira, Baret Merah, Clara, Aurora) ditanam menggunakan rancangan kelompok lengkap teracak dengan tiga ulangan. Hasil penelitian memperlihatkan bahwa varietas bayam hijau memiliki kandungan persentase warna hijau daun lebih banyak namun memiliki persentase warna biru dan merah yang lebih rendah dibandingkan varietas bayam merah. Hasil penelitian juga memperlihatkan bahwa varietas bayam hijau menghasilkan tinggi tanaman dan produktivitas yang lebih baik dibandingkan varietas bayam merah, namun varietas bayam merah menghasilkan luas daun dan jumlah daun per tanaman saat panen yang lebih baik besar dibandingkan varietas bayam hijau. Varietas White Leaf merupakan varietas bayam yang sangat baik karena memiliki persentase warna hijau daun yang tinggi, luas daun yang besar dan produktivitas yang tinggi. Spinach is one of the most important vegetables in Indonesia because it was the second most consumed after kangkung. Green spinach and red spinach are the most widely grown and consumed types of spinach. This study aimed to determine differences in growth and productivity between varieties of green spinach and red spinach. The research was conducted in February – April 2021 at the Leuwikopo Experimental Field, Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University. A total of nine varieties of green spinach and four varieties of red spinach were planted using a completely randomized block design with three replications. The results showed that the green spinach variety contained a higher percentage of green leaf color but had a lower percentage of blue and red leaf color than the red spinach varieties. The results also showed that the green spinach varieties produced better plant height and productivity than the red spinach varieties, but the red spinach produced better leaf area and a number of leaves per plant at harvest than the green spinach. The White Leaf variety is the excellent spinach variety because it has a high percentage of green leaf color, large leaf area, and high productivity.

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.